BiocParallel - Bioconductor facilities for parallel evaluation

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Last updated 2 months ago

infrastructurebioconductor-packagecore-packagecpp

17.13 score 67 stars 1.1k dependents 6.3k scripts 86k downloads

fgsea - Fast Gene Set Enrichment Analysis

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Last updated 2 days ago

geneexpressiondifferentialexpressiongenesetenrichmentpathwayscpp

16.25 score 380 stars 103 dependents 3.9k scripts 27k downloads

MultiAssayExperiment - Software for the integration of multi-omics experiments in Bioconductor

Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Last updated 1 days ago

infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcga

14.81 score 70 stars 125 dependents 670 scripts 9.2k downloads

mixOmics - Omics Data Integration Project

Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

Last updated 2 months ago

immunooncologymicroarraysequencingmetabolomicsmetagenomicsproteomicsgenepredictionmultiplecomparisonclassificationregressionbioconductorgenomicsgenomics-datagenomics-visualizationmultivariate-analysismultivariate-statisticsomicsr-pkgr-project

13.08 score 163 stars 20 dependents 1.3k scripts 4.0k downloads

Spectra - Spectra Infrastructure for Mass Spectrometry Data

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Last updated 4 days ago

infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry

12.86 score 39 stars 33 dependents 223 scripts 3.3k downloads

SingleR - Reference-Based Single-Cell RNA-Seq Annotation

Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

Last updated 1 days ago

softwaresinglecellgeneexpressiontranscriptomicsclassificationclusteringannotationbioconductorsinglercpp

12.54 score 179 stars 1 dependents 2.0k scripts 6.3k downloads

SpatialExperiment - S4 Class for Spatially Resolved -omics Data

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

Last updated 2 months ago

datarepresentationdataimportinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial

12.44 score 56 stars 63 dependents 1.3k scripts 6.9k downloads

scDblFinder - scDblFinder

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.

Last updated 2 months ago

preprocessingsinglecellrnaseqatacseqdoubletssingle-cell

12.35 score 166 stars 1 dependents 852 scripts 2.7k downloads

metagenomeSeq - Statistical analysis for sparse high-throughput sequencing

metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

Last updated 4 days ago

immunooncologyclassificationclusteringgeneticvariabilitydifferentialexpressionmicrobiomemetagenomicsnormalizationvisualizationmultiplecomparisonsequencingsoftware

12.17 score 68 stars 10 dependents 498 scripts 2.6k downloads

BiocSingular - Singular Value Decomposition for Bioconductor Packages

Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.

Last updated 2 months ago

softwaredimensionreductionprincipalcomponentbioconductor-packagehuman-cell-atlassingular-value-decompositioncpp

12.06 score 7 stars 98 dependents 1.0k scripts 22k downloads

sparseMatrixStats - Summary Statistics for Rows and Columns of Sparse Matrices

High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.

Last updated 2 months ago

infrastructuresoftwaredatarepresentationcpp

12.01 score 54 stars 131 dependents 178 scripts 27k downloads

OmnipathR - OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Last updated 2 months ago

graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteins

11.73 score 118 stars 2 dependents 236 scripts 1.1k downloads

MatrixGenerics - S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.

Last updated 2 months ago

infrastructuresoftwarebioconductor-packagecore-package

11.53 score 12 stars 1.3k dependents 124 scripts 74k downloads

QFeatures - Quantitative features for mass spectrometry data

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

Last updated 2 months ago

infrastructuremassspectrometryproteomicsmetabolomicsbioconductormass-spectrometry

11.45 score 25 stars 48 dependents 251 scripts 3.5k downloads

PCAtools - PCAtools: Everything Principal Components Analysis

Principal Component Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This 'summary' of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular - users can also identify optimal number of principal components via different metrics, such as elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.

Last updated 2 months ago

rnaseqatacseqgeneexpressiontranscriptionsinglecellprincipalcomponentcpp

11.27 score 333 stars 3 dependents 816 scripts 1.9k downloads

XVector - Foundation of external vector representation and manipulation in Bioconductor

Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).

Last updated 2 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

11.21 score 2 stars 1.7k dependents 67 scripts 99k downloads

decoupleR - decoupleR: Ensemble of computational methods to infer biological activities from omics data

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

Last updated 2 months ago

differentialexpressionfunctionalgenomicsgeneexpressiongeneregulationnetworksoftwarestatisticalmethodtranscription

11.13 score 202 stars 3 dependents 266 scripts 1.7k downloads

Maaslin2 - "Multivariable Association Discovery in Population-scale Meta-omics Studies"

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.

Last updated 2 months ago

metagenomicssoftwaremicrobiomenormalizationbiobakerybioconductordifferential-abundance-analysisfalse-discovery-ratemultiple-covariatespublicrepeated-measurestools

11.11 score 125 stars 4 dependents 524 scripts 1.6k downloads

infercnv - Infer Copy Number Variation from Single-Cell RNA-Seq Data

Using single-cell RNA-Seq expression to visualize CNV in cells.

Last updated 2 months ago

softwarecopynumbervariationvariantdetectionstructuralvariationgenomicvariationgeneticstranscriptomicsstatisticalmethodbayesianhiddenmarkovmodelsinglecelljagscpp

11.01 score 575 stars 652 scripts 2.4k downloads

basilisk - Freezing Python Dependencies Inside Bioconductor Packages

Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.

Last updated 2 months ago

infrastructurebioconductor-package

10.69 score 27 stars 37 dependents 73 scripts 5.5k downloads

MsCoreUtils - Core Utils for Mass Spectrometry Data

MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

Last updated 2 months ago

infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils

10.64 score 16 stars 68 dependents 41 scripts 5.9k downloads

ANCOMBC - Microbiome differential abudance and correlation analyses with bias correction

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.

Last updated 2 months ago

differentialexpressionmicrobiomenormalizationsequencingsoftwareancomancombcancombc2correlationdifferential-abundance-analysissecom

10.61 score 110 stars 1 dependents 408 scripts 2.3k downloads

scRepertoire - A toolkit for single-cell immune receptor profiling

scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.

Last updated 2 days ago

softwareimmunooncologysinglecellclassificationannotationsequencingcpp

10.54 score 312 stars 228 scripts 975 downloads

DECIPHER - Tools for curating, analyzing, and manipulating biological sequences

A toolset for deciphering and managing biological sequences.

Last updated 2 days ago

clusteringgeneticssequencingdataimportvisualizationmicroarrayqualitycontrolqpcralignmentwholegenomemicrobiomeimmunooncologygenepredictionopenmp

10.50 score 13 dependents 892 scripts 4.4k downloads

celda - CEllular Latent Dirichlet Allocation

Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.

Last updated 2 months ago

singlecellgeneexpressionclusteringsequencingbayesianimmunooncologydataimportcppopenmp

10.39 score 148 stars 2 dependents 265 scripts 1.5k downloads

Cardinal - A mass spectrometry imaging toolbox for statistical analysis

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

Last updated 3 days ago

softwareinfrastructureproteomicslipidomicsmassspectrometryimagingmassspectrometryimmunooncologynormalizationclusteringclassificationregression

10.30 score 42 stars 203 scripts 530 downloads

muscat - Multi-sample multi-group scRNA-seq data analysis tools

`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.

Last updated 2 months ago

immunooncologydifferentialexpressionsequencingsinglecellsoftwarestatisticalmethodvisualization

10.23 score 169 stars 686 scripts 1.0k downloads

scuttle - Single-Cell RNA-Seq Analysis Utilities

Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

Last updated 2 months ago

immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationtranscriptomicsgeneexpressionsequencingsoftwaredataimportopenblascpp

10.20 score 78 dependents 1.7k scripts 17k downloads

MOFA2 - Multi-Omics Factor Analysis v2

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

Last updated 2 months ago

dimensionreductionbayesianvisualizationfactor-analysismofamulti-omics

10.17 score 308 stars 482 scripts 888 downloads

miloR - Differential neighbourhood abundance testing on a graph

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using either a negative bionomial generalized linear model or negative binomial generalized linear mixed model.

Last updated 2 months ago

singlecellmultiplecomparisonfunctionalgenomicssoftwareopenblascppopenmp

10.16 score 345 stars 334 scripts 740 downloads

plotgardener - Coordinate-Based Genomic Visualization Package for R

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Last updated 2 months ago

visualizationgenomeannotationfunctionalgenomicsgenomeassemblyhiccpp

10.15 score 303 stars 3 dependents 163 scripts 434 downloads

singleCellTK - Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

Last updated 2 months ago

singlecellgeneexpressiondifferentialexpressionalignmentclusteringimmunooncologybatcheffectnormalizationqualitycontroldataimportgui

10.09 score 181 stars 194 scripts 685 downloads

UCSC.utils - Low-level utilities to retrieve data from the UCSC Genome Browser

A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.

Last updated 2 months ago

infrastructuregenomeassemblyannotationgenomeannotationdataimportbioconductor-packagecore-package

10.03 score 1 stars 1.7k dependents 4 scripts 53k downloads

tradeSeq - trajectory-based differential expression analysis for sequencing data

tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.

Last updated 2 months ago

clusteringregressiontimecoursedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization

10.00 score 240 stars 416 scripts 1.1k downloads

rhdf5filters - HDF5 Compression Filters

Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications.

Last updated 2 months ago

infrastructuredataimportcompressionfilter-pluginhdf5

9.91 score 5 stars 235 dependents 4 scripts 33k downloads

ggtreeExtra - An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.

Last updated 2 months ago

softwarevisualizationphylogeneticsannotation

9.86 score 88 stars 3 dependents 394 scripts 1.5k downloads

MicrobiotaProcess - A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).

Last updated 2 months ago

visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data

9.78 score 183 stars 1 dependents 130 scripts 697 downloads

RTCGAToolbox - A new tool for exporting TCGA Firehose data

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Last updated 3 days ago

differentialexpressiongeneexpressionsequencing

9.75 score 18 stars 5 dependents 76 scripts 769 downloads

cytomapper - Visualization of highly multiplexed imaging data in R

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

Last updated 2 months ago

immunooncologysoftwaresinglecellonechanneltwochannelmultiplecomparisonnormalizationdataimportbioimagingimaging-mass-cytometrysingle-cellspatial-analysis

9.70 score 31 stars 5 dependents 360 scripts 607 downloads

InteractiveComplexHeatmap - Make Interactive Complex Heatmaps

This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.

Last updated 2 months ago

softwarevisualizationsequencinginteractive-heatmaps

9.68 score 130 stars 4 dependents 128 scripts 700 downloads

Nebulosa - Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.

Last updated 2 months ago

softwaregeneexpressionsinglecellvisualizationdimensionreductionsingle-cellsingle-cell-analysissingle-cell-multiomicssingle-cell-rna-seq

9.63 score 89 stars 518 scripts 1.9k downloads

pcaExplorer - Interactive Visualization of RNA-seq Data Using a Principal Components Approach

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

Last updated 2 days ago

immunooncologyvisualizationrnaseqdimensionreductionprincipalcomponentqualitycontrolguireportwritingshinyappsbioconductorprincipal-componentsreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly

9.63 score 56 stars 180 scripts 794 downloads

clustifyr - Classifier for Single-cell RNA-seq Using Cell Clusters

Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.

Last updated 2 months ago

singlecellannotationsequencingmicroarraygeneexpressionassign-identitiesclustersmarker-genesrna-seqsingle-cell-rna-seq

9.60 score 113 stars 294 scripts 282 downloads

MetaboCoreUtils - Core Utils for Metabolomics Data

MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.

Last updated 2 months ago

infrastructuremetabolomicsmassspectrometrymass-spectrometry

9.58 score 9 stars 34 dependents 55 scripts 3.0k downloads

scMerge - scMerge: Merging multiple batches of scRNA-seq data

Like all gene expression data, single-cell data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell data.

Last updated 2 months ago

batcheffectgeneexpressionnormalizationrnaseqsequencingsinglecellsoftwaretranscriptomicsbioinformaticssingle-cell

9.51 score 67 stars 1 dependents 135 scripts 908 downloads

tidybulk - Brings transcriptomics to the tidyverse

This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

Last updated 2 months ago

assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsbioconductorbulk-transcriptional-analysesdeseq2differential-expressionedgerensembl-idsentrezgene-symbolsgseamds-dimensionspcapiperedundancytibbletidytidy-datatidyversetranscriptstsne

9.47 score 166 stars 1 dependents 169 scripts 546 downloads

ProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages

S4 generic functions and classes needed by Bioconductor proteomics packages.

Last updated 4 days ago

infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics

9.44 score 8 stars 189 dependents 5 scripts 19k downloads

bluster - Clustering Algorithms for Bioconductor

Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.

Last updated 2 months ago

immunooncologysoftwaregeneexpressiontranscriptomicssinglecellclusteringcpp

9.40 score 47 dependents 632 scripts 9.5k downloads

SpatialFeatureExperiment - Integrating SpatialExperiment with Simple Features in sf

A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.

Last updated 2 days ago

datarepresentationtranscriptomicsspatial

9.34 score 44 stars 1 dependents 290 scripts 381 downloads

ggmsa - Plot Multiple Sequence Alignment using 'ggplot2'

A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.

Last updated 2 days ago

softwarevisualizationalignmentannotationmultiplesequencealignment

9.33 score 205 stars 2 dependents 195 scripts 859 downloads

MassSpecWavelet - Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See <doi:10.1093/bioinformatics/btl355} for further details.

Last updated 4 days ago

immunooncologymassspectrometryproteomicspeakdetection

9.25 score 8 stars 15 dependents 36 scripts 3.3k downloads

sesame - SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.

Last updated 1 days ago

dnamethylationmethylationarraypreprocessingqualitycontrolbioinformaticsdna-methylationmicroarray

9.22 score 65 stars 1 dependents 278 scripts 1.4k downloads

EWCE - Expression Weighted Celltype Enrichment

Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

Last updated 2 months ago

geneexpressiontranscriptiondifferentialexpressiongenesetenrichmentgeneticsmicroarraymrnamicroarrayonechannelrnaseqbiomedicalinformaticsproteomicsvisualizationfunctionalgenomicssinglecelldeconvolutionsingle-cellsingle-cell-rna-seqtranscriptomics

9.16 score 54 stars 96 scripts 501 downloads

schex - Hexbin plots for single cell omics data

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.

Last updated 2 months ago

softwaresequencingsinglecelldimensionreductionvisualizationimmunooncologydataimport

9.10 score 73 stars 2 dependents 95 scripts 380 downloads

CARNIVAL - A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

Last updated 2 months ago

transcriptomicsgeneexpressionnetworkcausal-modelsfootprintsinteger-linear-programmingpathway-enrichment-analysis

9.03 score 57 stars 1 dependents 89 scripts 270 downloads

batchelor - Single-Cell Batch Correction Methods

Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.

Last updated 2 months ago

sequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectnormalizationcpp

8.96 score 7 dependents 1.2k scripts 6.5k downloads

scp - Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

Last updated 2 months ago

geneexpressionproteomicssinglecellmassspectrometrypreprocessingcellbasedassaysbioconductormass-spectrometrysingle-cellsoftware

8.85 score 21 stars 116 scripts 404 downloads

BayesSpace - Clustering and Resolution Enhancement of Spatial Transcriptomes

Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Last updated 2 months ago

softwareclusteringtranscriptomicsgeneexpressionsinglecellimmunooncologydataimportopenblascppopenmp

8.82 score 113 stars 1 dependents 260 scripts 530 downloads

tidySingleCellExperiment - Brings SingleCellExperiment to the Tidyverse

'tidySingleCellExperiment' is an adapter that abstracts the 'SingleCellExperiment' container in the form of a 'tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a 'tidySingleCellExperiment' is directly compatible with functions from 'tidyverse' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).

Last updated 2 months ago

assaydomaininfrastructurernaseqdifferentialexpressionsinglecellgeneexpressionnormalizationclusteringqualitycontrolsequencingbioconductordplyrggplot2plotlysingle-cell-rna-seqsingle-cell-sequencingsinglecellexperimenttibbletidyrtidyverse

8.78 score 36 stars 2 dependents 103 scripts 342 downloads

bambu - Context-Aware Transcript Quantification from Long Read RNA-Seq data

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

Last updated 2 months ago

alignmentcoveragedifferentialexpressionfeatureextractiongeneexpressiongenomeannotationgenomeassemblyimmunooncologylongreadmultiplecomparisonnormalizationrnaseqregressionsequencingsoftwaretranscriptiontranscriptomicsbambubioconductorlong-readsnanoporenanopore-sequencingrna-seqrna-seq-analysistranscript-quantificationtranscript-reconstructioncpp

8.77 score 190 stars 1 dependents 87 scripts 691 downloads

BiocBaseUtils - General utility functions for developing Bioconductor packages

The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.

Last updated 2 months ago

softwareinfrastructurebioconductor-packagecore-package

8.77 score 4 stars 155 dependents 3 scripts 11k downloads

cmapR - CMap Tools in R

The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.

Last updated 2 months ago

dataimportdatarepresentationgeneexpressionbioconductorbioinformaticscmap

8.77 score 86 stars 254 scripts 794 downloads

CellBench - Construct Benchmarks for Single Cell Analysis Methods

This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.

Last updated 2 months ago

softwareinfrastructuresinglecellbenchmarkbioinformatics

8.71 score 30 stars 98 scripts 248 downloads

memes - motif matching, comparison, and de novo discovery using the MEME Suite

A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.

Last updated 2 months ago

dataimportfunctionalgenomicsgeneregulationmotifannotationmotifdiscoverysequencematchingsoftware

8.64 score 46 stars 1 dependents 113 scripts 424 downloads

FRASER - Find RAre Splicing Events in RNA-Seq Data

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

Last updated 2 months ago

rnaseqalternativesplicingsequencingsoftwaregeneticscoverageaberrant-splicingdiagnosticsoutlier-detectionrare-diseaserna-seqsplicingopenblascpp

8.61 score 39 stars 158 scripts 274 downloads

SPOTlight - `SPOTlight`: Spatial Transcriptomics Deconvolution

`SPOTlight`provides a method to deconvolute spatial transcriptomics spots using a seeded NMF approach along with visualization tools to assess the results. Spatially resolved gene expression profiles are key to understand tissue organization and function. However, novel spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots).

Last updated 2 months ago

singlecellspatialstatisticalmethod

8.61 score 164 stars 177 scripts 436 downloads

Banksy - Spatial transcriptomic clustering

Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.

Last updated 2 months ago

clusteringspatialsinglecellgeneexpressiondimensionreductionclustering-algorithmsingle-cell-omicsspatial-omics

8.52 score 74 stars 86 scripts 297 downloads

tidySummarizedExperiment - Brings SummarizedExperiment to the Tidyverse

The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.

Last updated 2 months ago

assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomics

8.52 score 25 stars 1 dependents 194 scripts 615 downloads

projectR - Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

Last updated 2 months ago

functionalpredictiongeneregulationbiologicalquestionsoftware

8.49 score 62 stars 67 scripts 177 downloads

SPIAT - Spatial Image Analysis of Tissues

SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

Last updated 2 months ago

biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization

8.43 score 21 stars 66 scripts 302 downloads

cBioPortalData - Exposes and Makes Available Data from the cBioPortal Web Resources

The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.

Last updated 1 days ago

softwareinfrastructurethirdpartyclientbioconductor-package

8.38 score 31 stars 4 dependents 148 scripts 644 downloads

assorthead - Assorted Header-Only C++ Libraries

Vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.

Last updated 9 hours ago

singlecellqualitycontrolnormalizationdatarepresentationdataimportdifferentialexpressionalignment

8.37 score 162 dependents 5.3k downloads

dreamlet - Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of these data, complex study designs, and low read count per cell mean that characterizing cell type specific molecular mechanisms requires a user-frieldly, purpose-build analytical framework. We have developed the dreamlet package that applies a pseudobulk approach and fits a regression model for each gene and cell cluster to test differential expression across individuals associated with a trait of interest. Use of precision-weighted linear mixed models enables accounting for repeated measures study designs, high dimensional batch effects, and varying sequencing depth or observed cells per biosample.

Last updated 2 months ago

rnaseqgeneexpressiondifferentialexpressionbatcheffectqualitycontrolregressiongenesetenrichmentgeneregulationepigeneticsfunctionalgenomicstranscriptomicsnormalizationsinglecellpreprocessingsequencingimmunooncologysoftwarecpp

8.33 score 12 stars 124 scripts 198 downloads

netZooR - Unified methods for the inference and analysis of gene regulatory networks

netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.

Last updated 2 months ago

networkinferencenetworkgeneregulationgeneexpressiontranscriptionmicroarraygraphandnetworkgene-regulatory-networktranscription-factors

8.28 score 102 stars 104 scripts 168 downloads

PSMatch - Handling and Managing Peptide Spectrum Matches

The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

Last updated 2 months ago

infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches

8.24 score 3 stars 38 dependents 15 scripts 2.5k downloads

ggkegg - Analyzing and visualizing KEGG information using the grammar of graphics

This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.

Last updated 2 months ago

pathwaysdataimportkeggggplot2ggraphpathwaytidygraphvisualization

8.23 score 216 stars 1 dependents 29 scripts 706 downloads

GeneTonic - Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.

Last updated 2 days ago

guigeneexpressionsoftwaretranscriptiontranscriptomicsvisualizationdifferentialexpressionpathwaysreportwritinggenesetenrichmentannotationgoshinyappsbioconductorbioconductor-packagedata-explorationdata-visualizationfunctional-enrichment-analysisgene-expressionpathway-analysisreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly

8.23 score 76 stars 1 dependents 37 scripts 538 downloads

crisprDesign - Comprehensive design of CRISPR gRNAs for nucleases and base editors

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

Last updated 2 months ago

crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design

8.23 score 20 stars 3 dependents 78 scripts 292 downloads

ngsReports - Load FastqQC reports and other NGS related files

This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.

Last updated 2 months ago

qualitycontrolreportwriting

8.19 score 22 stars 98 scripts 233 downloads

sccomp - Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

Last updated 2 months ago

bayesianregressiondifferentialexpressionsinglecellbatch-correctioncompositioncytofdifferential-proportionmicrobiomemultilevelproportionsrandom-effectssingle-cellunwanted-variation

8.18 score 94 stars 60 scripts 195 downloads

hypeR - An R Package For Geneset Enrichment Workflows

An R Package for Geneset Enrichment Workflows.

Last updated 2 months ago

genesetenrichmentannotationpathwaysbioinformaticscomputational-biologygeneset-enrichment-analysis

8.18 score 76 stars 132 scripts 238 downloads

ExploreModelMatrix - Graphical Exploration of Design Matrices

Given a sample data table and a design formula, ExploreModelMatrix generates an interactive application for exploration of the resulting design matrix. This can be helpful for interpreting model coefficients and constructing appropriate contrasts in (generalized) linear models. Static visualizations can also be generated.

Last updated 12 hours ago

experimentaldesignregressiondifferentialexpressionshinyapps

8.14 score 36 stars 79 scripts 326 downloads

nullranges - Generation of null ranges via bootstrapping or covariate matching

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.

Last updated 2 months ago

visualizationgenesetenrichmentfunctionalgenomicsepigeneticsgeneregulationgenetargetgenomeannotationannotationgenomewideassociationhistonemodificationchipseqatacseqdnaseseqrnaseqhiddenmarkovmodelbioconductorbootstrapgenomicsmatchingstatistics

8.12 score 26 stars 1 dependents 47 scripts 358 downloads

compcodeR - RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

Last updated 10 hours ago

immunooncologyrnaseqdifferentialexpression

8.06 score 11 stars 26 scripts 280 downloads

velociraptor - Toolkit for Single-Cell Velocity

This package provides Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data. We use the basilisk package to manage Conda environments, and the zellkonverter package to convert data structures between SingleCellExperiment (R) and AnnData (Python). The information produced by the velocity methods is stored in the various components of the SingleCellExperiment class.

Last updated 2 months ago

singlecellgeneexpressionsequencingcoveragerna-velocity

8.05 score 55 stars 45 scripts 304 downloads

rBLAST - R Interface for the Basic Local Alignment Search Tool

Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

Last updated 2 months ago

geneticssequencingsequencematchingalignmentdataimportbioconductorbioinformaticsblast-search

8.04 score 105 stars 100 scripts 258 downloads

simplifyEnrichment - Simplify Functional Enrichment Results

A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.

Last updated 2 months ago

softwarevisualizationgoclusteringgenesetenrichment

7.99 score 112 stars 191 scripts 1.5k downloads

TOAST - Tools for the analysis of heterogeneous tissues

This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. tree-based differential analysis 3. improve variable selection in reference-free deconvolution 4. partial reference-free deconvolution with prior knowledge.

Last updated 2 months ago

dnamethylationgeneexpressiondifferentialexpressiondifferentialmethylationmicroarraygenetargetepigeneticsmethylationarray

7.98 score 10 stars 3 dependents 105 scripts 784 downloads

hermes - Preprocessing, analyzing, and reporting of RNA-seq data

Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.

Last updated 2 months ago

rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering

7.87 score 10 stars 1 dependents 49 scripts 382 downloads

lemur - Latent Embedding Multivariate Regression

Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.

Last updated 2 months ago

transcriptomicsdifferentialexpressionsinglecelldimensionreductionregressionopenblascpp

7.86 score 82 stars 80 scripts 160 downloads

monaLisa - Binned Motif Enrichment Analysis and Visualization

Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.

Last updated 2 months ago

motifannotationvisualizationfeatureextractionepigenetics

7.84 score 38 stars 50 scripts 302 downloads

LACE - Longitudinal Analysis of Cancer Evolution (LACE)

LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.

Last updated 2 months ago

biomedicalinformaticssinglecellsomaticmutation

7.83 score 15 stars 3 scripts 376 downloads

biodb - biodb, a library and a development framework for connecting to chemical and biological databases

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Last updated 2 months ago

softwareinfrastructuredataimportkeggbiologycheminformaticschemistrydatabasescpp

7.82 score 11 stars 6 dependents 22 scripts 432 downloads

mistyR - Multiview Intercellular SpaTial modeling framework

mistyR is an implementation of the Multiview Intercellular SpaTialmodeling framework (MISTy). MISTy is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data. MISTy facilitates an in-depth understanding of marker interactions by profiling the intra- and intercellular relationships. MISTy is a flexible framework able to process a custom number of views. Each of these views can describe a different spatial context, i.e., define a relationship among the observed expressions of the markers, such as intracellular regulation or paracrine regulation, but also, the views can also capture cell-type specific relationships, capture relations between functional footprints or focus on relations between different anatomical regions. Each MISTy view is considered as a potential source of variability in the measured marker expressions. Each MISTy view is then analyzed for its contribution to the total expression of each marker and is explained in terms of the interactions with other measurements that led to the observed contribution.

Last updated 2 months ago

softwarebiomedicalinformaticscellbiologysystemsbiologyregressiondecisiontreesinglecellspatialbioconductorbiologyintercellularmachine-learningmodularmolecular-biologymultiviewspatial-transcriptomics

7.81 score 50 stars 160 scripts 225 downloads

rrvgo - Reduce + Visualize GO

Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.

Last updated 2 months ago

annotationclusteringgonetworkpathwayssoftware

7.79 score 22 stars 176 scripts 880 downloads

TreeSummarizedExperiment - TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.

Last updated 2 months ago

datarepresentationinfrastructure

7.79 score 15 dependents 225 scripts 3.0k downloads

target - Predict Combined Function of Transcription Factors

Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) <doi: 10.1038/nprot.2013.150>. Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.

Last updated 2 months ago

softwarestatisticalmethodtranscriptionalgorithmchip-seqdna-bindinggene-regulationtranscription-factors

7.78 score 4 stars 1.3k scripts 192 downloads

BioNERO - Biological Network Reconstruction Omnibus

BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.

Last updated 2 months ago

softwaregeneexpressiongeneregulationsystemsbiologygraphandnetworkpreprocessingnetworknetworkinference

7.76 score 25 stars 1 dependents 43 scripts 711 downloads

FLAMES - FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

Last updated 3 days ago

rnaseqsinglecelltranscriptomicsdataimportdifferentialsplicingalternativesplicinggeneexpressionlongreadzlibcurlbzip2xz-utilscpp

7.76 score 24 stars 11 scripts 326 downloads

dittoSeq - User Friendly Single-Cell and Bulk RNA Sequencing Visualization

A universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. Visualizations include dimensionality reduction plots, heatmaps, scatterplots, percent composition or expression across groups, and more. Customizations range from size and title adjustments to automatic generation of annotations for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton plot, hidden data overlay upon cursor hovering via ggplotly conversion, and many more. All with simple, discrete inputs. Color blindness friendliness is powered by legend adjustments (enlarged keys), and by allowing the use of shapes or letter-overlay in addition to the carefully selected dittoColors().

Last updated 2 months ago

softwarevisualizationrnaseqsinglecellgeneexpressiontranscriptomicsdataimport

7.76 score 2 dependents 804 scripts 2.4k downloads

PhyloProfile - PhyloProfile

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Last updated 2 days ago

softwarevisualizationdatarepresentationmultiplecomparisonfunctionalpredictiondimensionreductionbioinformaticsheatmapinteractive-visualizationsorthologsphylogenetic-profileshiny

7.76 score 33 stars 10 scripts 212 downloads

baySeq - Empirical Bayesian analysis of patterns of differential expression in count data

This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

Last updated 2 months ago

sequencingdifferentialexpressionmultiplecomparisonsagebayesiancoverage

7.75 score 3 dependents 79 scripts 882 downloads

ScaledMatrix - Creating a DelayedMatrix of Scaled and Centered Values

Provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale() function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication.

Last updated 2 months ago

softwaredatarepresentation

7.75 score 100 dependents 8 scripts 21k downloads

fishpond - Fishpond: downstream methods and tools for expression data

Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.

Last updated 2 months ago

sequencingrnaseqgeneexpressiontranscriptionnormalizationregressionmultiplecomparisonbatcheffectvisualizationdifferentialexpressiondifferentialsplicingalternativesplicingsinglecellbioconductorgene-expressiongenomicssalmonscrnaseqstatisticstranscriptomics

7.75 score 27 stars 150 scripts 600 downloads

SpatialDecon - Deconvolution of mixed cells from spatial and/or bulk gene expression data

Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.

Last updated 2 months ago

immunooncologyfeatureextractiongeneexpressiontranscriptomicsspatial

7.75 score 33 stars 57 scripts 388 downloads

pathwayPCA - Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>; Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.

Last updated 2 months ago

copynumbervariationdnamethylationgeneexpressionsnptranscriptiongenepredictiongenesetenrichmentgenesignalinggenetargetgenomewideassociationgenomicvariationcellbiologyepigeneticsfunctionalgenomicsgeneticslipidomicsmetabolomicsproteomicssystemsbiologytranscriptomicsclassificationdimensionreductionfeatureextractionprincipalcomponentregressionsurvivalmultiplecomparisonpathways

7.74 score 11 stars 42 scripts 170 downloads

countsimQC - Compare Characteristic Features of Count Data Sets

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

Last updated 9 hours ago

microbiomernaseqsinglecellexperimentaldesignqualitycontrolreportwritingvisualizationimmunooncology

7.69 score 27 stars 24 scripts 454 downloads

MsFeatures - Functionality for Mass Spectrometry Features

The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages.

Last updated 2 months ago

infrastructuremassspectrometrymetabolomics

7.67 score 7 stars 12 dependents 30 scripts 2.1k downloads

imcRtools - Methods for imaging mass cytometry data analysis

This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.

Last updated 2 months ago

immunooncologysinglecellspatialdataimportclusteringimcsingle-cell

7.62 score 22 stars 125 scripts 402 downloads

igvShiny - igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.

Last updated 2 months ago

softwareshinyappssequencingcoverage

7.60 score 37 stars 119 scripts 122 downloads

ggsc - Visualizing Single Cell and Spatial Transcriptomics

Useful functions to visualize single cell and spatial data. It supports visualizing 'Seurat', 'SingleCellExperiment' and 'SpatialExperiment' objects through grammar of graphics syntax implemented in 'ggplot2'.

Last updated 2 months ago

dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualizationopenblascppopenmp

7.58 score 43 stars 18 scripts 178 downloads

crisprScore - On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.

Last updated 2 months ago

crisprfunctionalgenomicsfunctionalpredictionbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomicsgrnagrna-sequencegrna-sequencesscoring-algorithmsgrnasgrna-design

7.56 score 15 stars 4 dependents 19 scripts 318 downloads

RBioFormats - R interface to Bio-Formats

An R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

Last updated 2 months ago

dataimportbio-formatsbioconductorimage-processingopenjdk

7.53 score 24 stars 1 dependents 52 scripts 342 downloads

MsExperiment - Infrastructure for Mass Spectrometry Experiments

Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.

Last updated 2 months ago

infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport

7.53 score 5 stars 14 dependents 105 scripts 2.0k downloads

scDesign3 - A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics

We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.

Last updated 2 months ago

softwaresinglecellsequencinggeneexpressionspatial

7.51 score 87 stars 25 scripts 146 downloads

MOSim - Multi-Omics Simulation (MOSim)

MOSim package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups.

Last updated 2 months ago

softwaretimecourseexperimentaldesignrnaseqcpp

7.51 score 9 stars 6 scripts 194 downloads

EpiCompare - Comparison, Benchmarking & QC of Epigenomic Datasets

EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.

Last updated 2 months ago

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsatacseqdnaseseqbenchmarkbenchmarkingbioconductorbioconductor-packagecomparisonhtmlinteractive-reporting

7.51 score 13 stars 46 scripts 76 downloads

animalcules - Interactive microbiome analysis toolkit

animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.

Last updated 2 months ago

microbiomemetagenomicscoveragevisualization

7.51 score 52 stars 22 scripts 546 downloads

proDA - Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Account for missing values in label-free mass spectrometry data without imputation. The package implements a probabilistic dropout model that ensures that the information from observed and missing values are properly combined. It adds empirical Bayesian priors to increase power to detect differentially abundant proteins.

Last updated 2 months ago

proteomicsmassspectrometrydifferentialexpressionbayesianregressionsoftwarenormalizationqualitycontrol

7.48 score 18 stars 1 dependents 47 scripts 378 downloads

cola - A Framework for Consensus Partitioning

Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.

Last updated 2 months ago

clusteringgeneexpressionclassificationsoftwareconsensus-clusteringcpp

7.46 score 59 stars 109 scripts 253 downloads

lipidr - Data Mining and Analysis of Lipidomics Datasets

lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.

Last updated 2 months ago

lipidomicsmassspectrometrynormalizationqualitycontrolvisualizationbioconductor

7.44 score 29 stars 40 scripts 289 downloads

Wrench - Wrench normalization for sparse count data

Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.

Last updated 2 months ago

normalizationsequencingsoftware

7.44 score 6 stars 11 dependents 9 scripts 2.3k downloads

orthogene - Interspecies gene mapping

`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.

Last updated 2 months ago

geneticscomparativegenomicspreprocessingphylogeneticstranscriptomicsgeneexpressionanimal-modelsbioconductorbioconductor-packagebioinformaticsbiomedicinecomparative-genomicsevolutionary-biologygenesgenomicsontologiestranslational-research

7.43 score 40 stars 1 dependents 25 scripts 524 downloads

scDiagnostics - Cell type annotation diagnostics

The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.

Last updated 2 months ago

annotationclassificationclusteringgeneexpressionrnaseqsinglecellsoftwaretranscriptomics

7.42 score 3 stars 46 scripts

GenomicDistributions - GenomicDistributions: fast analysis of genomic intervals with Bioconductor

If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.

Last updated 2 months ago

softwaregenomeannotationgenomeassemblydatarepresentationsequencingcoveragefunctionalgenomicsvisualization

7.40 score 24 stars 25 scripts 246 downloads

eisaR - Exon-Intron Split Analysis (EISA) in R

Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.

Last updated 2 months ago

transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq

7.37 score 15 stars 63 scripts 298 downloads

methylSig - MethylSig: Differential Methylation Testing for WGBS and RRBS Data

MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.

Last updated 2 months ago

dnamethylationdifferentialmethylationepigeneticsregressionmethylseqdifferential-methylationdna-methylation

7.37 score 17 stars 23 scripts 201 downloads

mbkmeans - Mini-batch K-means Clustering for Single-Cell RNA-seq

Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.

Last updated 2 months ago

clusteringgeneexpressionrnaseqsoftwaretranscriptomicssequencingsinglecellhuman-cell-atlascpp

7.37 score 9 stars 2 dependents 54 scripts 834 downloads

koinar - KoinaR - Remote machine learning inference using Koina

A client to simplify fetching predictions from the Koina web service. Koina is a model repository enabling the remote execution of models. Predictions are generated as a response to HTTP/S requests, the standard protocol used for nearly all web traffic.

Last updated 2 days ago

massspectrometryproteomicsinfrastructuresoftwarebioinformaticsdeep-learningmachine-learningmass-spectrometrypython

7.36 score 32 stars 4 scripts 92 downloads

scry - Small-Count Analysis Methods for High-Dimensional Data

Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.

Last updated 2 months ago

dimensionreductiongeneexpressionnormalizationprincipalcomponentrnaseqsoftwaresequencingsinglecelltranscriptomics

7.34 score 19 stars 116 scripts 568 downloads

PeacoQC - Peak-based selection of high quality cytometry data

This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.

Last updated 2 months ago

flowcytometryqualitycontrolpreprocessingpeakdetection

7.34 score 15 stars 3 dependents 27 scripts 404 downloads

nnSVG - Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.

Last updated 2 months ago

spatialsinglecelltranscriptomicsgeneexpressionpreprocessing

7.34 score 14 stars 1 dependents 130 scripts 271 downloads

scMultiSim - Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions

scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.

Last updated 2 months ago

singlecelltranscriptomicsgeneexpressionsequencingexperimentaldesign

7.31 score 22 stars 13 scripts 112 downloads

TBSignatureProfiler - Profile RNA-Seq Data Using TB Pathway Signatures

Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.

Last updated 3 days ago

geneexpressiondifferentialexpressionbioconductor-packagebiomarkersgene-signaturestuberculosis

7.28 score 12 stars 20 scripts 178 downloads

crisprBase - Base functions and classes for CRISPR gRNA design

Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

Last updated 2 months ago

crisprfunctionalgenomicsbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequences

7.27 score 5 stars 6 dependents 52 scripts 309 downloads

tidytof - Analyze High-dimensional Cytometry Data Using Tidy Data Principles

This package implements an interactive, scientific analysis pipeline for high-dimensional cytometry data built using tidy data principles. It is specifically designed to play well with both the tidyverse and Bioconductor software ecosystems, with functionality for reading/writing data files, data cleaning, preprocessing, clustering, visualization, modeling, and other quality-of-life functions. tidytof implements a "grammar" of high-dimensional cytometry data analysis.

Last updated 2 months ago

singlecellflowcytometrybioinformaticscytometrydata-sciencesingle-celltidyversecpp

7.26 score 19 stars 35 scripts 116 downloads

CaDrA - Candidate Driver Analysis

Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA's main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.

Last updated 2 months ago

microarrayrnaseqgeneexpressionsoftwarefeatureextraction

7.26 score 24 stars 12 scripts 109 downloads

GeomxTools - NanoString GeoMx Tools

Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.

Last updated 2 months ago

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial

7.25 score 3 dependents 219 scripts 754 downloads

CHETAH - Fast and accurate scRNA-seq cell type identification

CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate, selective and fast scRNA-seq classifier. Classification is guided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classification tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to "intermediate types": more general classifications that ended in an intermediate node of the tree.

Last updated 2 months ago

classificationrnaseqsinglecellclusteringgeneexpressionimmunooncology

7.25 score 42 stars 70 scripts 218 downloads

cosmosR - COSMOS (Causal Oriented Search of Multi-Omic Space)

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.

Last updated 2 months ago

cellbiologypathwaysnetworkproteomicsmetabolomicstranscriptomicsgenesignalingdata-integrationmetabolomic-datanetwork-modellingphosphoproteomics

7.21 score 58 stars 35 scripts 188 downloads

signatureSearch - Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

This package implements algorithms and data structures for performing gene expression signature (GES) searches, and subsequently interpreting the results functionally with specialized enrichment methods.

Last updated 2 months ago

softwaregeneexpressiongokeggnetworkenrichmentsequencingcoveragedifferentialexpressioncpp

7.18 score 17 stars 1 dependents 74 scripts 369 downloads

TnT - Interactive Visualization for Genomic Features

A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.

Last updated 2 months ago

infrastructurevisualizationbioconductorgenome-browserhtmlwidgetsshiny

7.15 score 14 stars 17 scripts 130 downloads

iSEEu - iSEE Universe

iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

Last updated 2 months ago

immunooncologyvisualizationguidimensionreductionfeatureextractionclusteringtranscriptiongeneexpressiontranscriptomicssinglecellcellbasedassayshacktoberfest

7.15 score 9 stars 1 dependents 35 scripts 265 downloads

basilisk.utils - Basilisk Installation Utilities

Implements utilities for installation of the basilisk package, primarily for creation of the underlying Conda instance. This allows us to avoid re-writing the same R code in both the configure script (for centrally administered R installations) and in the lazy installation mechanism (for distributed package binaries). It is highly unlikely that developers - or, heaven forbid, end-users! - will need to interact with this package directly; they should be using the basilisk package instead.

Last updated 2 months ago

infrastructure

7.14 score 38 dependents 7 scripts 4.9k downloads

SPsimSeq - Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

Last updated 2 months ago

geneexpressionrnaseqsinglecellsequencingdnaseq

7.13 score 10 stars 1 dependents 28 scripts 403 downloads

AlpsNMR - Automated spectraL Processing System for NMR

Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.

Last updated 2 months ago

softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport

7.11 score 15 stars 12 scripts 269 downloads

treeclimbR - An algorithm to find optimal signal levels in a tree

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

Last updated 2 months ago

statisticalmethodcellbasedassays

7.11 score 19 stars 45 scripts 164 downloads

HiCExperiment - Bioconductor class for interacting with Hi-C files in R

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.

Last updated 2 months ago

hicdna3dstructuredataimport

7.10 score 9 stars 2 dependents 47 scripts 256 downloads

msqrob2 - Robust statistical inference for quantitative LC-MS proteomics

msqrob2 provides a robust linear mixed model framework for assessing differential abundance in MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or summarised protein expression values. The model parameter estimates can be stabilized by ridge regression, empirical Bayes variance estimation and robust M-estimation. msqrob2's hurde workflow can handle missing data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed data.

Last updated 2 days ago

proteomicsmassspectrometrydifferentialexpressionmultiplecomparisonregressionexperimentaldesignsoftwareimmunooncologynormalizationtimecoursepreprocessing

7.08 score 10 stars 85 scripts 300 downloads

TADCompare - TADCompare: Identification and characterization of differential TADs

TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.

Last updated 2 months ago

softwarehicsequencingfeatureextractionclustering

7.04 score 23 stars 9 scripts 238 downloads

systemPipeShiny - systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS’ current functionalities include: (a) interactive creation of experimental designs and metadata using an easy to use tabular editor or file uploader; (b) visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows; (d) access to a wide range of data processing routines; (e) and an extendable set of visualization functionalities. Complex visual results can be managed on a 'Canvas Workbench’ allowing users to organize and to compare plots in an efficient manner combined with a session snapshot feature to continue work at a later time. The present suite of pre-configured visualization examples. The modular design of SPR makes it easy to design custom functions without any knowledge of Shiny, as well as extending the environment in the future with contributions from the community.

Last updated 2 months ago

shinyappsinfrastructuredataimportsequencingqualitycontrolreportwritingexperimentaldesignclusteringbioconductorbioconductor-packagedata-visualizationshinysystempiper

7.04 score 34 stars 36 scripts 192 downloads

cardelino - Clone Identification from Single Cell Data

Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

Last updated 2 months ago

singlecellrnaseqvisualizationtranscriptomicsgeneexpressionsequencingsoftwareexomeseqclonal-clusteringgibbs-samplingscrna-seqsingle-cellsomatic-mutations

7.04 score 59 stars 62 scripts 250 downloads

gDRcore - Processing functions and interface to process and analyze drug dose-response data

This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.

Last updated 4 days ago

softwareshinyappscpp

7.04 score 1 stars 1 dependents 4 scripts 144 downloads

MsBackendMsp - Mass Spectrometry Data Backend for NIST msp Files

Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.

Last updated 2 months ago

infrastructureproteomicsmassspectrometrymetabolomicsdataimportmass-spectrometry

7.03 score 5 stars 2 dependents 36 scripts 395 downloads

SharedObject - Sharing R objects across multiple R processes without memory duplication

This package is developed for facilitating parallel computing in R. It is capable to create an R object in the shared memory space and share the data across multiple R processes. It avoids the overhead of memory dulplication and data transfer, which make sharing big data object across many clusters possible.

Last updated 2 months ago

infrastructuresharedobjectcpp

7.03 score 45 stars 1 dependents 5 scripts 266 downloads

lfa - Logistic Factor Analysis for Categorical Data

Logistic Factor Analysis is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter. The main method estimates genetic population structure from genotype data. There are also methods for estimating individual-specific allele frequencies using the population structure. Lastly, a structured Hardy-Weinberg equilibrium (HWE) test is developed, which quantifies the goodness of fit of the genotype data to the estimated population structure, via the estimated individual-specific allele frequencies (all of which generalizes traditional HWE tests).

Last updated 2 months ago

snpdimensionreductionprincipalcomponentregressionopenblas

7.03 score 16 stars 1 dependents 56 scripts 638 downloads

pipeComp - pipeComp pipeline benchmarking framework

A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

Last updated 2 months ago

geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq

7.02 score 41 stars 43 scripts 168 downloads

COCOA - Coordinate Covariation Analysis

COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.

Last updated 2 months ago

epigeneticsdnamethylationatacseqdnaseseqmethylseqmethylationarrayprincipalcomponentgenomicvariationgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqsequencingimmunooncologydna-methylationpca

7.02 score 10 stars 21 scripts 230 downloads

methrix - Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

Last updated 2 months ago

dnamethylationsequencingcoveragebedgraphbioinformaticsdna-methylation

7.01 score 30 stars 38 scripts 217 downloads

MetaboAnnotation - Utilities for Annotation of Metabolomics Data

High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

Last updated 4 days ago

infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry

7.00 score 15 stars 32 scripts 496 downloads

CuratedAtlasQueryR - Queries the Human Cell Atlas

Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.

Last updated 2 months ago

assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsdatabaseduckdbhdf5human-cell-atlassingle-cellsinglecellexperimenttidyverse

6.99 score 89 stars 37 scripts 137 downloads

GenomicSuperSignature - Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.

Last updated 2 months ago

transcriptomicssystemsbiologyprincipalcomponentrnaseqsequencingpathwaysclusteringbioconductor-packageexploratory-data-analysisgseameshprincipal-component-analysisrna-sequencing-profilestransferlearning

6.97 score 16 stars 59 scripts 202 downloads

dir.expiry - Managing Expiration for Cache Directories

Implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.

Last updated 2 months ago

softwareinfrastructure

6.97 score 40 dependents 6 scripts 5.2k downloads

satuRn - Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.

Last updated 2 months ago

regressionexperimentaldesigndifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization

6.95 score 20 stars 1 dependents 74 scripts 506 downloads

AlphaMissenseR - Accessing AlphaMissense Data Resources in R

The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.

Last updated 2 months ago

snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology

6.92 score 8 stars 10 scripts 144 downloads

SimBu - Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.

Last updated 2 months ago

softwarernaseqsinglecell

6.92 score 12 stars 29 scripts 368 downloads

cliqueMS - Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.

Last updated 2 months ago

metabolomicsmassspectrometrynetworknetworkinferencecpp

6.91 score 12 stars 25 scripts 194 downloads

tRNA - Analyzing tRNA sequences and structures

The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.

Last updated 2 months ago

softwarevisualizationbioconductorsequencesstructurestrna

6.91 score 1 stars 3 dependents 3 scripts 348 downloads

RCM - Fit row-column association models with the negative binomial distribution for the microbiome

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

Last updated 2 months ago

metagenomicsdimensionreductionmicrobiomevisualizationordinationphyloseqrcm

6.90 score 16 stars 25 scripts 149 downloads

CytoPipeline - Automation and visualization of flow cytometry data analysis pipelines

This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline.

Last updated 2 months ago

flowcytometrypreprocessingqualitycontrolworkflowstepimmunooncologysoftwarevisualization

6.90 score 3 stars 2 dependents 17 scripts 169 downloads

alevinQC - Generate QC Reports For Alevin Output

Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.

Last updated 10 hours ago

qualitycontrolsinglecellcpp

6.89 score 31 stars 21 scripts 359 downloads

musicatk - Mutational Signature Comprehensive Analysis Toolkit

Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

Last updated 2 months ago

softwarebiologicalquestionsomaticmutationvariantannotation

6.89 score 13 stars 17 scripts 238 downloads

scClassify - scClassify: single-cell Hierarchical Classification

scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.

Last updated 2 months ago

singlecellgeneexpressionclassification

6.88 score 22 stars 29 scripts 178 downloads

escheR - Unified multi-dimensional visualizations with Gestalt principles

The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.

Last updated 2 months ago

spatialsinglecelltranscriptomicsvisualizationsoftwaremultidimensionalsingle-cellspatial-omics

6.88 score 6 stars 1 dependents 141 scripts 198 downloads

MPRAnalyze - Statistical Analysis of MPRA data

MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.

Last updated 2 months ago

immunooncologysoftwarestatisticalmethodsequencinggeneexpressioncellbiologycellbasedassaysdifferentialexpressionexperimentaldesignclassification

6.86 score 12 stars 30 scripts 202 downloads

BioTIP - BioTIP: An R package for characterization of Biological Tipping-Point

Adopting tipping-point theory to transcriptome profiles to unravel disease regulatory trajectory.

Last updated 2 months ago

sequencingrnaseqgeneexpressiontranscriptionsoftware

6.84 score 18 stars 37 scripts 204 downloads

extraChIPs - Additional functions for working with ChIP-Seq data

This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

Last updated 2 months ago

chipseqhicsequencingcoverage

6.83 score 7 stars 25 scripts 229 downloads

peakPantheR - Peak Picking and Annotation of High Resolution Experiments

An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.

Last updated 2 months ago

massspectrometrymetabolomicspeakdetectionfeature-detectionmass-spectrometry

6.82 score 12 stars 23 scripts 172 downloads

cellxgenedp - Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal

The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.

Last updated 2 months ago

singlecelldataimportthirdpartyclient

6.79 score 8 stars 31 scripts 161 downloads

ideal - Interactive Differential Expression AnaLysis

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

Last updated 2 days ago

immunooncologygeneexpressiondifferentialexpressionrnaseqsequencingvisualizationqualitycontrolguigenesetenrichmentreportwritingshinyappsbioconductordifferential-expressionreproducible-researchrna-seqrna-seq-analysisshinyuser-friendly

6.78 score 29 stars 5 scripts 254 downloads

simona - Semantic Similarity on Bio-Ontologies

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

Last updated 2 months ago

softwareannotationgobiomedicalinformaticscpp

6.78 score 15 stars 1 dependents 27 scripts 239 downloads

VennDetail - A package for visualization and extract details

A set of functions to generate high-resolution Venn,Vennpie plot,extract and combine details of these subsets with user datasets in data frame is available.

Last updated 2 months ago

datarepresentationgraphandnetworkextractvenndiagram

6.75 score 29 stars 65 scripts 394 downloads

dcanr - Differential co-expression/association network analysis

This package implements methods and an evaluation framework to infer differential co-expression/association networks. Various methods are implemented and can be evaluated using simulated datasets. Inference of differential co-expression networks can allow identification of networks that are altered between two conditions (e.g., health and disease).

Last updated 2 months ago

networkinferencegraphandnetworkdifferentialexpressionnetwork

6.75 score 6 stars 1 dependents 26 scripts 269 downloads

sechm - sechm: Complex Heatmaps from a SummarizedExperiment

sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.

Last updated 2 months ago

geneexpressionvisualization

6.73 score 6 stars 2 dependents 50 scripts 250 downloads

metapod - Meta-Analyses on P-Values of Differential Analyses

Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.

Last updated 2 months ago

multiplecomparisondifferentialpeakcallingcpp

6.73 score 45 dependents 17 scripts 7.8k downloads

waddR - Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

The package offers statistical tests based on the 2-Wasserstein distance for detecting and characterizing differences between two distributions given in the form of samples. Functions for calculating the 2-Wasserstein distance and testing for differential distributions are provided, as well as a specifically tailored test for differential expression in single-cell RNA sequencing data.

Last updated 2 months ago

softwarestatisticalmethodsinglecelldifferentialexpressioncpp

6.70 score 25 stars 6 scripts 141 downloads

CoreGx - Classes and Functions to Serve as the Basis for Other 'Gx' Packages

A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.

Last updated 2 months ago

softwarepharmacogenomicsclassificationsurvival

6.69 score 6 dependents 55 scripts 591 downloads

nipalsMCIA - Multiple Co-Inertia Analysis via the NIPALS Method

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.

Last updated 3 days ago

softwareclusteringclassificationmultiplecomparisonnormalizationpreprocessingsinglecell

6.67 score 6 stars 7 scripts 117 downloads

AnVILBase - Generic functions for interacting with the AnVIL ecosystem

Provides generic functions for interacting with the AnVIL ecosystem. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers.

Last updated 2 months ago

softwareinfrastructure

6.67 score 13 dependents 70 scripts 154 downloads

MicrobiomeProfiler - An R/shiny package for microbiome functional enrichment analysis

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

Last updated 2 months ago

microbiomesoftwarevisualizationkegg

6.66 score 36 stars 17 scripts 258 downloads

proActiv - Estimate Promoter Activity from RNA-Seq data

Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.

Last updated 2 months ago

rnaseqgeneexpressiontranscriptionalternativesplicinggeneregulationdifferentialsplicingfunctionalgenomicsepigeneticstranscriptomicspreprocessingalternative-promotersgenomicspromoter-activitypromoter-annotationrna-seq-data

6.65 score 50 stars 15 scripts 192 downloads

distinct - distinct: a method for differential analyses via hierarchical permutation tests

distinct is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via hierarchical non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. While most methods for differential expression target differences in the mean abundance between conditions, distinct, by comparing full cdfs, identifies, both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean (e.g., unimodal vs. bi-modal distributions with the same mean). distinct is a general and flexible tool: due to its fully non-parametric nature, which makes no assumptions on how the data was generated, it can be applied to a variety of datasets. It is particularly suitable to perform differential state analyses on single cell data (i.e., differential analyses within sub-populations of cells), such as single cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. To use distinct one needs data from two or more groups of samples (i.e., experimental conditions), with at least 2 samples (i.e., biological replicates) per group.

Last updated 2 months ago

geneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationsinglecellflowcytometrygenetargetopenblascpp

6.65 score 11 stars 1 dependents 34 scripts 508 downloads

tidyomics - Easily install and load the tidyomics ecosystem

The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.

Last updated 2 months ago

assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicscytometrygenomicstidyverse

6.64 score 63 stars 5 scripts 166 downloads

ggspavis - Visualization functions for spatial transcriptomics data

Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.

Last updated 2 months ago

spatialsinglecelltranscriptomicsgeneexpressionqualitycontroldimensionreduction

6.64 score 2 stars 218 scripts 354 downloads

scAnnotatR - Pretrained learning models for cell type prediction on single cell RNA-sequencing data

The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.

Last updated 2 months ago

singlecelltranscriptomicsgeneexpressionsupportvectormachineclassificationsoftware

6.64 score 15 stars 16 scripts 486 downloads

syntenet - Inference And Analysis Of Synteny Networks

syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.

Last updated 4 days ago

softwarenetworkinferencefunctionalgenomicscomparativegenomicsphylogeneticssystemsbiologygraphandnetworkwholegenomenetworkcomparative-genomicsevolutionary-genomicsnetwork-sciencephylogenomicssyntenysynteny-networkcpp

6.64 score 24 stars 1 dependents 12 scripts 210 downloads

Modstrings - Working with modified nucleotide sequences

Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

Last updated 2 months ago

dataimportdatarepresentationinfrastructuresequencingsoftwarebioconductorbiostringsdnadna-modificationsmodified-nucleotidesnucleotidesrnarna-modification-alphabetrna-modificationssequences

6.64 score 1 stars 8 dependents 5 scripts 381 downloads

ViSEAGO - ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.

Last updated 4 days ago

softwareannotationgogenesetenrichmentmultiplecomparisonclusteringvisualization

6.62 score 21 scripts 241 downloads

CatsCradle - This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.

Last updated 2 months ago

biologicalquestionstatisticalmethodgeneexpressionsinglecelltranscriptomicsspatial

6.61 score 3 stars

PepsNMR - Pre-process 1H-NMR FID signals

This package provides R functions for common pre-procssing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.

Last updated 2 months ago

softwarepreprocessingvisualizationmetabolomicsdataimport

6.60 score 10 stars 1 dependents 22 scripts 342 downloads

CiteFuse - CiteFuse: multi-modal analysis of CITE-seq data

CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

Last updated 2 months ago

singlecellgeneexpressionbioinformaticssingle-cellcpp

6.59 score 27 stars 18 scripts 186 downloads

bayNorm - Single-cell RNA sequencing data normalization

bayNorm is used for normalizing single-cell RNA-seq data.

Last updated 2 months ago

immunooncologynormalizationrnaseqsinglecellsequencingscrnaseqcppopenmp

6.59 score 9 stars 36 scripts 326 downloads

miaSim - Microbiome Data Simulation

Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

Last updated 2 months ago

microbiomesoftwaresequencingdnaseqatacseqcoveragenetwork

6.57 score 18 stars 23 scripts 150 downloads

Statial - A package to identify changes in cell state relative to spatial associations

Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

Last updated 2 months ago

singlecellspatialclassificationsingle-cell

6.56 score 5 stars 20 scripts 180 downloads

SpectralTAD - SpectralTAD: Hierarchical TAD detection using spectral clustering

SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.

Last updated 2 months ago

softwarehicsequencingfeatureextractionclustering

6.53 score 8 stars 17 scripts 244 downloads

zenith - Gene set analysis following differential expression using linear (mixed) modeling with dream

Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().

Last updated 2 months ago

rnaseqgeneexpressiongenesetenrichmentdifferentialexpressionbatcheffectqualitycontrolregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationpreprocessingmicroarrayimmunooncologysoftware

6.52 score 1 dependents 91 scripts 238 downloads

tricycle - tricycle: Transferable Representation and Inference of cell cycle

The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.

Last updated 2 months ago

singlecellsoftwaretranscriptomicsrnaseqtranscriptionbiologicalquestiondimensionreductionimmunooncology

6.51 score 24 stars 45 scripts 490 downloads

RNAmodR - Detection of post-transcriptional modifications in high throughput sequencing data

RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.

Last updated 2 months ago

softwareinfrastructureworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsribomethseqrnarnamodr

6.51 score 3 stars 3 dependents 9 scripts 211 downloads

Moonlight2R - Identify oncogenes and tumor suppressor genes from omics data

The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments. An additional mechanistic layer evaluates if there are mutations affecting the protein stability of the transcription factors (TFs) of the TSGs and OCGs, as that may have an effect on the expression of the genes.

Last updated 4 days ago

dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksurvivalgenesetenrichmentnetworkenrichment

6.50 score 5 stars 42 scripts 136 downloads

dominoSignal - Cell Communication Analysis for Single Cell RNA Sequencing

dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.

Last updated 2 months ago

systemsbiologysinglecelltranscriptomicsnetwork

6.50 score 3 stars 5 scripts 115 downloads

bugsigdbr - R-side access to published microbial signatures from BugSigDB

The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.

Last updated 2 months ago

dataimportgenesetenrichmentmetagenomicsmicrobiomebioconductor-package

6.49 score 3 stars 46 scripts 201 downloads

CBNplot - plot bayesian network inferred from gene expression data based on enrichment analysis results

This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.

Last updated 2 months ago

visualizationbayesiangeneexpressionnetworkinferencepathwaysreactomenetworknetworkenrichmentgenesetenrichment

6.49 score 62 stars 9 scripts 258 downloads

methylclock - Methylclock - DNA methylation-based clocks

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

Last updated 2 months ago

dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp

6.48 score 39 stars 26 scripts 332 downloads

scds - In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

In single cell RNA sequencing (scRNA-seq) data combinations of cells are sometimes considered a single cell (doublets). The scds package provides methods to annotate doublets in scRNA-seq data computationally.

Last updated 2 months ago

singlecellrnaseqqualitycontrolpreprocessingtranscriptomicsgeneexpressionsequencingsoftwareclassification

6.48 score 1 dependents 144 scripts 930 downloads

coMethDMR - Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.

Last updated 2 months ago

dnamethylationepigeneticsmethylationarraydifferentialmethylationgenomewideassociation

6.47 score 7 stars 42 scripts 198 downloads

alabaster.ranges - Load and Save Ranges-related Artifacts from File

Save GenomicRanges, IRanges and related data structures into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 2 months ago

dataimportdatarepresentation

6.46 score 7 dependents 8 scripts 4.0k downloads

recountmethylation - Access and analyze public DNA methylation array data compilations

Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.

Last updated 2 months ago

dnamethylationepigeneticsmicroarraymethylationarrayexperimenthub

6.45 score 9 stars 9 scripts 220 downloads

alabaster.se - Load and Save SummarizedExperiments from File

Save SummarizedExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 2 months ago

dataimportdatarepresentation

6.45 score 6 dependents 8 scripts 3.9k downloads

NanoStringNCTools - NanoString nCounter Tools

Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data.

Last updated 2 months ago

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseq

6.44 score 4 dependents 91 scripts 642 downloads

SpotClean - SpotClean adjusts for spot swapping in spatial transcriptomics data

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

Last updated 2 months ago

dataimportrnaseqsequencinggeneexpressionspatialsinglecelltranscriptomicspreprocessingrna-seqspatial-transcriptomics

6.43 score 25 stars 36 scripts 190 downloads

TileDBArray - Using TileDB as a DelayedArray Backend

Implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.

Last updated 2 months ago

datarepresentationinfrastructuresoftware

6.41 score 10 stars 26 scripts 148 downloads

SpliceWiz - interactive analysis and visualization of alternative splicing in R

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.

Last updated 2 months ago

softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp

6.41 score 16 stars 8 scripts 311 downloads

chromstaR - Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.

Last updated 5 days ago

immunooncologysoftwaredifferentialpeakcallinghiddenmarkovmodelchipseqhistonemodificationmultiplecomparisonsequencingpeakdetectionatacseqcppopenmp

6.40 score 8 stars 10 scripts 344 downloads

MSstatsShiny - MSstats GUI for Statistical Anaylsis of Proteomics Experiments

MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.

Last updated 2 months ago

immunooncologymassspectrometryproteomicssoftwareshinyappsdifferentialexpressiononechanneltwochannelnormalizationqualitycontrolgui

6.40 score 14 stars 4 scripts 218 downloads

tanggle - Visualization of Phylogenetic Networks

Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <doi:10.1093/bioinformatics/btq706>.

Last updated 2 months ago

softwarevisualizationphylogeneticsalignmentclusteringmultiplesequencealignmentdataimport

6.40 score 11 stars 38 scripts 160 downloads

PrInCE - Predicting Interactomes from Co-Elution

PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.

Last updated 2 months ago

proteomicssystemsbiologynetworkinference

6.38 score 8 stars 25 scripts 168 downloads

artMS - Analytical R tools for Mass Spectrometry

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Last updated 2 months ago

proteomicsdifferentialexpressionbiomedicalinformaticssystemsbiologymassspectrometryannotationqualitycontrolgenesetenrichmentclusteringnormalizationimmunooncologymultiplecomparisonanalysisanalyticalap-msbioconductorbioinformaticsmass-spectrometryphosphoproteomicspost-translational-modificationquantitative-analysis

6.37 score 14 stars 12 scripts 206 downloads

miQC - Flexible, probabilistic metrics for quality control of scRNA-seq data

Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA encoded genes (mtDNA) and (ii) if a small number of genes are detected. miQC is data-driven QC metric that jointly models both the proportion of reads mapping to mtDNA and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset.

Last updated 2 months ago

singlecellqualitycontrolgeneexpressionpreprocessingsequencing

6.36 score 18 stars 63 scripts 239 downloads

concordexR - Identify Spatial Homogeneous Regions with concordex

Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.

Last updated 2 months ago

singlecellclusteringspatialtranscriptomics

6.34 score 13 stars 17 scripts 164 downloads

CellMixS - Evaluate Cellspecific Mixing

CellMixS provides metrics and functions to evaluate batch effects, data integration and batch effect correction in single cell trancriptome data with single cell resolution. Results can be visualized and summarised on different levels, e.g. on cell, celltype or dataset level.

Last updated 2 months ago

singlecelltranscriptomicsgeneexpressionbatcheffect

6.34 score 7 stars 63 scripts 182 downloads

gscreend - Analysis of pooled genetic screens

Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation.

Last updated 2 months ago

softwarestatisticalmethodpooledscreenscrispr

6.34 score 11 stars 7 scripts 138 downloads

mosdef - MOSt frequently used and useful Differential Expression Functions

This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

Last updated 2 days ago

geneexpressionsoftwaretranscriptiontranscriptomicsdifferentialexpressionvisualizationreportwritinggenesetenrichmentgo

6.33 score 4 dependents 323 downloads

rhinotypeR - Rhinovirus genotyping

"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.

Last updated 2 months ago

sequencinggeneticsphylogenetics

6.33 score 4 stars 2 scripts

gypsum - Interface to the gypsum REST API

Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

Last updated 2 months ago

dataimport

6.32 score 1 dependents 20 scripts 3.5k downloads

scFeatures - scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.

Last updated 2 months ago

cellbasedassayssinglecellspatialsoftwaretranscriptomics

6.31 score 10 stars 15 scripts 146 downloads

BSgenomeForge - Forge your own BSgenome data package

A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.

Last updated 2 months ago

infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationsequencingalignmentdataimportsequencematchingbioconductor-packagecore-package

6.30 score 4 stars 4 scripts 244 downloads

Herper - The Herper package is a simple toolset to install and manage conda packages and environments from R

Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.

Last updated 2 months ago

infrastructuresoftware

6.29 score 5 stars 52 scripts 250 downloads

RCX - R package implementing the Cytoscape Exchange (CX) format

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

Last updated 2 months ago

pathwaysdataimportnetwork

6.28 score 8 stars 1 dependents 10 scripts 150 downloads

timeOmics - Time-Course Multi-Omics data integration

timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group. The main steps of timeOmics are: 1. Plaform and time-specific normalization and filtering steps; 2. Modelling each biological into one time expression profile; 3. Clustering features with the same expression profile over time; 4. Post-hoc validation step.

Last updated 2 months ago

clusteringfeatureextractiontimecoursedimensionreductionsoftwaresequencingmicroarraymetabolomicsmetagenomicsproteomicsclassificationregressionimmunooncologygenepredictionmultiplecomparisonclusterintegrationmulti-omicstime-series

6.28 score 24 stars 10 scripts 202 downloads

signifinder - Collection and implementation of public transcriptional cancer signatures

signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.

Last updated 5 days ago

geneexpressiongenetargetimmunooncologybiomedicalinformaticsrnaseqmicroarrayreportwritingvisualizationsinglecellspatialgenesignaling

6.27 score 7 stars 16 scripts 126 downloads

pgxRpi - R wrapper for Progenetix

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

Last updated 2 months ago

copynumbervariationgenomicvariationdataimportsoftware

6.25 score 3 stars 21 scripts 130 downloads

scPCA - Sparse Contrastive Principal Component Analysis

A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA's ability to disentangle biological signal from unwanted variation through the use of control data. Also implements and extends cPCA.

Last updated 2 months ago

principalcomponentgeneexpressiondifferentialexpressionsequencingmicroarrayrnaseqbioconductorcontrastive-learningdimensionality-reduction

6.24 score 12 stars 29 scripts 204 downloads

CopyNumberPlots - Create Copy-Number Plots using karyoploteR functionality

CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.

Last updated 2 months ago

visualizationcopynumbervariationcoverageonechanneldataimportsequencingdnaseqbioconductorbioconductor-packagebioinformaticscopy-number-variationgenomicsgenomics-visualization

6.24 score 6 stars 2 dependents 16 scripts 272 downloads

RAIDS - Accurate Inference of Genetic Ancestry from Cancer Sequences

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

Last updated 2 months ago

geneticssoftwaresequencingwholegenomeprincipalcomponentgeneticvariabilitydimensionreductionbiocviewsancestrycancer-genomicsexome-sequencinggenomicsinferencer-languagerna-seqrna-sequencingwhole-genome-sequencing

6.23 score 5 stars 19 scripts 104 downloads

doubletrouble - Identification and classification of duplicated genes

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Last updated 2 months ago

softwarewholegenomecomparativegenomicsfunctionalgenomicsphylogeneticsnetworkclassificationbioinformaticscomparative-genomicsgene-duplicationmolecular-evolutionwhole-genome-duplication

6.23 score 11 stars 17 scripts 175 downloads

scMET - Bayesian modelling of cell-to-cell DNA methylation heterogeneity

High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this task. scMET is a hierarchical Bayesian model which overcomes sparsity, sharing information across cells and genomic features to robustly quantify genuine biological heterogeneity. scMET can identify highly variable features that drive epigenetic heterogeneity, and perform differential methylation and variability analyses. We illustrate how scMET facilitates the characterization of epigenetically distinct cell populations and how it enables the formulation of novel hypotheses on the epigenetic regulation of gene expression.

Last updated 2 months ago

immunooncologydnamethylationdifferentialmethylationdifferentialexpressiongeneexpressiongeneregulationepigeneticsgeneticsclusteringfeatureextractionregressionbayesiansequencingcoveragesinglecellbayesian-inferencegeneralised-linear-modelsheterogeneityhierarchical-modelsmethylation-analysissingle-cellcpp

6.23 score 20 stars 42 scripts 124 downloads

SBGNview - "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.

Last updated 2 months ago

genetargetpathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing

6.22 score 25 stars 22 scripts 374 downloads

StructuralVariantAnnotation - Variant annotations for structural variants

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Last updated 2 months ago

dataimportsequencingannotationgeneticsvariantannotation

6.21 score 2 dependents 91 scripts 606 downloads

biscuiteer - Convenience Functions for Biscuit

A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

Last updated 2 months ago

dataimportmethylseqdnamethylation

6.20 score 5 stars 16 scripts 270 downloads

scDataviz - scDataviz: single cell dataviz and downstream analyses

In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease.

Last updated 2 months ago

singlecellimmunooncologyrnaseqgeneexpressiontranscriptionflowcytometrymassspectrometrydataimport

6.20 score 61 stars 13 scripts 198 downloads

SingleMoleculeFootprinting - Analysis tools for Single Molecule Footprinting (SMF) data

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

Last updated 2 months ago

dnamethylationcoveragenucleosomepositioningdatarepresentationepigeneticsmethylseqqualitycontrolsequencing

6.20 score 2 stars 25 scripts 182 downloads

MOMA - Multi Omic Master Regulator Analysis

This package implements the inference of candidate master regulator proteins from multi-omics' data (MOMA) algorithm, as well as ancillary analysis and visualization functions.

Last updated 2 months ago

softwarenetworkenrichmentnetworkinferencenetworkfeatureextractionclusteringfunctionalgenomicstranscriptomicssystemsbiology

6.19 score 6 stars 13 scripts 147 downloads

alabaster.schemas - Schemas for the Alabaster Framework

Stores all schemas required by various alabaster.* packages. No computation should be performed by this package, as that is handled by alabaster.base. We use a separate package instead of storing the schemas in alabaster.base itself, to avoid conflating management of the schemas with code maintenence.

Last updated 2 months ago

datarepresentationdataimport

6.17 score 15 dependents 3.3k downloads

iNETgrate - Integrates DNA methylation data with gene expression in a single gene network

The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.

Last updated 2 months ago

geneexpressionrnaseqdnamethylationnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdimensionreductionprincipalcomponentmrnamicroarraynormalizationgenepredictionkeggsurvivalcore-services

6.16 score 73 stars 1 scripts 121 downloads

idpr - Profiling and Analyzing Intrinsically Disordered Proteins in R

‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages. Described in McFadden WM & Yanowitz JL (2022). "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PloS one, 17(4), e0266929. <https://doi.org/10.1371/journal.pone.0266929>.

Last updated 2 months ago

structuralpredictionproteomicscellbiology

6.16 score 4 stars 20 scripts 168 downloads

HIPPO - Heterogeneity-Induced Pre-Processing tOol

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

Last updated 2 months ago

sequencingsinglecellgeneexpressiondifferentialexpressionclustering

6.16 score 18 stars 4 scripts 130 downloads

ceRNAnetsim - Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.

Last updated 2 months ago

networkinferencesystemsbiologynetworkgraphandnetworktranscriptomicscernamirnanetwork-biologynetwork-simulatortcgatidygraphtidyverse

6.16 score 4 stars 12 scripts 118 downloads

crisprViz - Visualization Functions for CRISPR gRNAs

Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

Last updated 2 months ago

crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-analysiscrispr-designgrnagrna-sequencegrna-sequencessgrnasgrna-designvisualization

6.16 score 6 stars 2 dependents 6 scripts 190 downloads

dearseq - Differential Expression Analysis for RNA-seq data through a robust variance component test

Differential Expression Analysis RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data. Methods are detailed in: i) Agniel D & Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2020) dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, NAR Genomics and Bioinformatics, 2(4):lqaa093.

Last updated 2 months ago

biomedicalinformaticscellbiologydifferentialexpressiondnaseqgeneexpressiongeneticsgenesetenrichmentimmunooncologykeggregressionrnaseqsequencingsystemsbiologytimecoursetranscriptiontranscriptomics

6.14 score 7 stars 1 dependents 11 scripts 585 downloads

struct - Statistics in R Using Class-based Templates

Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. The templates can be used and where needed extended to 'wrap' tools and methods from other packages into a common standardised structure to allow for effective and fast integration. Model objects can be combined into sequences, and sequences nested in iterators using overloaded operators to simplify and improve readability of the code. Ontology lookup has been integrated and implemented to provide standardised definitions for methods, inputs and outputs wrapped using the class-based templates.

Last updated 2 months ago

workflowstep

6.14 score 3 dependents 76 scripts 276 downloads

CaMutQC - An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation.

Last updated 2 months ago

softwarequalitycontrolgenetargetcancer-genomicssomatic-mutations

6.14 score 7 stars 1 scripts 158 downloads

paxtoolsr - Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database. Pathway Commons is a project by the Memorial Sloan-Kettering Cancer Center (MSKCC), Dana-Farber Cancer Institute (DFCI), and the University of Toronto. Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.

Last updated 5 days ago

genesetenrichmentgraphandnetworkpathwayssoftwaresystemsbiologynetworkenrichmentnetworkreactomekeggopenjdk

6.12 score 10 stars 58 scripts 288 downloads

GPA - GPA (Genetic analysis incorporating Pleiotropy and Annotation)

This package provides functions for fitting GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy information and annotation data. In addition, it also includes ShinyGPA, an interactive visualization toolkit to investigate pleiotropic architecture.

Last updated 2 months ago

softwarestatisticalmethodclassificationgenomewideassociationsnpgeneticsclusteringmultiplecomparisonpreprocessinggeneexpressiondifferentialexpressioncpp

6.11 score 13 stars 7 scripts 139 downloads

simpleSeg - A package to perform simple cell segmentation

Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.

Last updated 2 months ago

classificationsurvivalsinglecellnormalizationspatialspatial-statistics

6.11 score 2 dependents 18 scripts 164 downloads

structToolbox - Data processing & analysis tools for Metabolomics and other omics

An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning. This toolbox allows the user to build extensive and standardised workflows for data analysis. The methods and tools have been implemented using class-based templates provided by the struct (Statistics in R Using Class-based Templates) package. The toolbox includes pre-processing methods (e.g. signal drift and batch correction, normalisation, missing value imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and PLS, including cross-validation and permutation testing) as well as machine learning methods (e.g. Support Vector Machines). The STATistics Ontology (STATO) has been integrated and implemented to provide standardised definitions for the different methods, inputs and outputs.

Last updated 2 months ago

workflowstepmetabolomicsbioconductor-packagedimslc-msmachine-learningmultivariate-analysisstatisticsunivariate

6.11 score 9 stars 12 scripts 210 downloads

knowYourCG - Functional analysis of DNA methylome datasets

KnowYourCG (KYCG) is a supervised learning framework designed for the functional analysis of DNA methylation data. Unlike existing tools that focus on genes or genomic intervals, KnowYourCG directly targets CpG dinucleotides, featuring automated supervised screenings of diverse biological and technical influences, including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type-specific methylation, and trait associations. KnowYourCG addresses the challenges of data sparsity in various methylation datasets, including low-pass Nanopore sequencing, single-cell DNA methylomes, 5-hydroxymethylation profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies and epigenetic clocks.

Last updated 1 days ago

epigeneticsdnamethylationsequencingsinglecellspatialmethylationarray

6.10 score 2 stars 2 scripts 107 downloads

peco - A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data.

Last updated 2 months ago

sequencingrnaseqgeneexpressiontranscriptomicssinglecellsoftwarestatisticalmethodclassificationvisualizationcell-cyclesingle-cell-rna-seq

6.09 score 12 stars 34 scripts 144 downloads

cogeqc - Systematic quality checks on comparative genomics analyses

cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.

Last updated 2 months ago

softwaregenomeassemblycomparativegenomicsfunctionalgenomicsphylogeneticsqualitycontrolnetworkcomparative-genomicsevolutionary-genomics

6.09 score 8 stars 17 scripts 158 downloads

MoleculeExperiment - Prioritising a molecule-level storage of Spatial Transcriptomics Data

MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.

Last updated 2 months ago

dataimportdatarepresentationinfrastructuresoftwarespatialtranscriptomics

6.08 score 12 stars 8 scripts 128 downloads

IgGeneUsage - Differential gene usage in immune repertoires

Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.

Last updated 2 months ago

differentialexpressionregressiongeneticsbayesianbiomedicalinformaticsimmunooncologymathematicalbiologyb-cell-receptorbcr-repertoiredifferential-analysisdifferential-gene-expressionhigh-throughput-sequencingimmune-repertoireimmune-repertoire-analysisimmune-repertoiresimmunogenomicsimmunoglobulinimmunoinformaticsimmunological-bioinformaticsimmunologytcr-repertoirevdj-recombinationcpp

6.08 score 6 stars 1 scripts 143 downloads

shiny.gosling - A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny

A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. http://gosling-lang.org/. This R package is based on gosling.js. It uses R functions to create gosling plots that could be embedded onto R Shiny apps.

Last updated 2 months ago

shinyappsgeneticsvisualization

6.08 score 1 dependents 53 scripts 120 downloads

tidySpatialExperiment - SpatialExperiment with tidy principles

tidySpatialExperiment provides a bridge between the SpatialExperiment package and the tidyverse ecosystem. It creates an invisible layer that allows you to interact with a SpatialExperiment object as if it were a tibble; enabling the use of functions from dplyr, tidyr, ggplot2 and plotly. But, underneath, your data remains a SpatialExperiment object.

Last updated 2 months ago

infrastructurernaseqgeneexpressionsequencingspatialtranscriptomicssinglecell

6.07 score 6 stars 12 scripts 146 downloads

GloScope - Population-level Representation on scRNA-Seq data

This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots.

Last updated 2 months ago

datarepresentationqualitycontrolrnaseqsequencingsoftwaresinglecell

6.07 score 3 stars 87 scripts 164 downloads

raer - RNA editing tools in R

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

Last updated 2 months ago

multiplecomparisonrnaseqsinglecellsequencingcoverageepitranscriptomicsfeatureextractionannotationalignmentbioconductor-packagerna-seq-analysissingle-cell-analysissingle-cell-rna-seqcurlbzip2xz-utilszlib

6.05 score 7 stars 6 scripts 122 downloads

VERSO - Viral Evolution ReconStructiOn (VERSO)

Mutations that rapidly accumulate in viral genomes during a pandemic can be used to track the evolution of the virus and, accordingly, unravel the viral infection network. To this extent, sequencing samples of the virus can be employed to estimate models from genomic epidemiology and may serve, for instance, to estimate the proportion of undetected infected people by uncovering cryptic transmissions, as well as to predict likely trends in the number of infected, hospitalized, dead and recovered people. VERSO is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a log-likelihood function. VERSO includes two separate and subsequent steps; in this package we provide an R implementation of VERSO STEP 1.

Last updated 2 months ago

biomedicalinformaticssequencingsomaticmutation

6.05 score 7 stars 144 downloads

metaseqR2 - An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Last updated 2 months ago

softwaregeneexpressiondifferentialexpressionworkflowsteppreprocessingqualitycontrolnormalizationreportwritingrnaseqtranscriptionsequencingtranscriptomicsbayesianclusteringcellbiologybiomedicalinformaticsfunctionalgenomicssystemsbiologyimmunooncologyalternativesplicingdifferentialsplicingmultiplecomparisontimecoursedataimportatacseqepigeneticsregressionproprietaryplatformsgenesetenrichmentbatcheffectchipseq

6.05 score 7 stars 4 scripts 202 downloads

vissE - Visualising Set Enrichment Analysis Results

This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches.

Last updated 2 months ago

softwaregeneexpressiongenesetenrichmentnetworkenrichmentnetworkbioinformatics

6.05 score 13 stars 19 scripts 224 downloads

TrajectoryUtils - Single-Cell Trajectory Analysis Utilities

Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.

Last updated 2 months ago

geneexpressionsinglecell

6.04 score 9 dependents 15 scripts 3.0k downloads

CluMSID - Clustering of MS2 Spectra for Metabolite Identification

CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.

Last updated 2 months ago

metabolomicspreprocessingclustering

6.04 score 10 stars 22 scripts 176 downloads

MOGAMUN - MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

MOGAMUN is a multi-objective genetic algorithm that identifies active modules in a multiplex biological network. This allows analyzing different biological networks at the same time. MOGAMUN is based on NSGA-II (Non-Dominated Sorting Genetic Algorithm, version II), which we adapted to work on networks.

Last updated 2 months ago

systemsbiologygraphandnetworkdifferentialexpressionbiomedicalinformaticstranscriptomicsclusteringnetwork

6.03 score 12 stars 5 scripts 152 downloads

CRISPRball - Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

A Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.

Last updated 3 days ago

softwareshinyappscrisprqualitycontrolvisualizationguicrispr-screendata-visualizationinteractive-visualizationsmageckplotlyscreeningshiny

6.03 score 9 stars 24 scripts 127 downloads

scanMiR - scanMiR

A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

Last updated 2 months ago

mirnasequencematchingalignment

6.03 score 1 dependents 51 scripts 220 downloads

omicsViewer - Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer

omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existing ExpressionSet object. The pure dependency on R/Bioconductor guarantees maximum flexibility in the statistical analysis in the back-end. Once the ExpressionSet is prepared, it can be visualized using the front-end, implemented by shiny and plotly. Both features and samples could be selected from (data) tables or graphs (scatter plot/heatmap). Different types of analyses, such as enrichment analysis (using Bioconductor package fgsea or fisher's exact test) and STRING network analysis, will be performed on the fly and the results are visualized simultaneously. When a subset of samples and a phenotype variable is selected, a significance test on means (t-test or ranked based test; when phenotype variable is quantitative) or test of independence (chi-square or fisher’s exact test; when phenotype data is categorical) will be performed to test the association between the phenotype of interest with the selected samples. Additionally, other analyses can be easily added as extra shiny modules. Therefore, omicsViewer will greatly facilitate data exploration, many different hypotheses can be explored in a short time without the need for knowledge of R. In addition, the resulting data could be easily shared using a shiny server. Otherwise, a standalone version of omicsViewer together with designated omics data could be easily created by integrating it with portable R, which can be shared with collaborators or submitted as supplementary data together with a manuscript.

Last updated 2 months ago

softwarevisualizationgenesetenrichmentdifferentialexpressionmotifdiscoverynetworknetworkenrichment

6.02 score 4 stars 22 scripts 168 downloads

phantasusLite - Loading and annotation RNA-seq counts matrices

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

Last updated 2 months ago

geneexpressiontranscriptomicsrnaseq

6.02 score 7 stars 1 dependents 8 scripts 124 downloads

gemini - GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press).

Last updated 2 months ago

softwarecrisprbayesiandataimportcomputational-biologygenetic-interactions

6.02 score 15 stars 9 scripts 132 downloads

faers - R interface for FDA Adverse Event Reporting System

The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.

Last updated 2 months ago

softwaredataimportbiomedicalinformaticspharmacogenomicsadverse-eventsdrug-safetyfaersfaers-procedurepharmacovigilancesignal-detection

6.02 score 16 stars 5 scripts 184 downloads

StabMap - Stabilised mosaic single cell data integration using unshared features

StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists.

Last updated 2 months ago

singlecelldimensionreductionsoftware

6.00 score 60 scripts 83 downloads

HiContacts - Analysing cool files in R with HiContacts

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

Last updated 2 months ago

hicdna3dstructure

5.99 score 10 stars 49 scripts 225 downloads

RiboCrypt - Interactive visualization in genomics

R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development.

Last updated 2 months ago

softwaresequencingriboseqrnaseq

5.98 score 5 stars 19 scripts 158 downloads

Dino - Normalization of Single-Cell mRNA Sequencing Data

Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.

Last updated 2 months ago

softwarenormalizationrnaseqsinglecellsequencinggeneexpressiontranscriptomicsregressioncellbasedassays

5.97 score 8 stars 13 scripts 164 downloads

GeoTcgaData - Processing Various Types of Data on GEO and TCGA

Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

Last updated 2 months ago

geneexpressiondifferentialexpressionrnaseqcopynumbervariationmicroarraysoftwarednamethylationdifferentialmethylationsnpatacseqmethylationarray

5.96 score 24 stars 19 scripts 354 downloads

BiocFHIR - Illustration of FHIR ingestion and transformation using R

FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

Last updated 2 months ago

infrastructuredataimportdatarepresentationfhir

5.95 score 4 stars 15 scripts 122 downloads

atena - Analysis of Transposable Elements

Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.

Last updated 2 months ago

transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomics

5.95 score 9 stars 1 scripts 360 downloads

FEAST - FEAture SelcTion (FEAST) for Single-cell clustering

Cell clustering is one of the most important and commonly performed tasks in single-cell RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select a subset of genes (referred to as “features”), whose expression patterns will then be used for downstream clustering. A good set of features should include the ones that distinguish different cell types, and the quality of such set could have significant impact on the clustering accuracy. FEAST is an R library for selecting most representative features before performing the core of scRNA-seq clustering. It can be used as a plug-in for the etablished clustering algorithms such as SC3, TSCAN, SHARP, SIMLR, and Seurat. The core of FEAST algorithm includes three steps: 1. consensus clustering; 2. gene-level significance inference; 3. validation of an optimized feature set.

Last updated 2 months ago

sequencingsinglecellclusteringfeatureextraction

5.95 score 10 stars 45 scripts 230 downloads

Rhisat2 - R Wrapper for HISAT2 Aligner

An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

Last updated 10 hours ago

alignmentsequencingsplicedalignmentcpp

5.95 score 3 stars 1 dependents 7 scripts 482 downloads

transformGamPoi - Variance Stabilizing Transformation for Gamma-Poisson Models

Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., 'acosh', 'log(x+1)'), (2) model residual based (Pearson and randomized quantile residuals).

Last updated 2 months ago

singlecellnormalizationpreprocessingregressioncpp

5.95 score 21 stars 21 scripts 185 downloads

escape - Easy single cell analysis platform for enrichment

A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells.

Last updated 2 months ago

softwaresinglecellclassificationannotationgenesetenrichmentsequencinggenesignalingpathways

5.95 score 147 scripts 772 downloads

ClustIRR - Clustering of immune receptor repertoires

ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment.

Last updated 17 hours ago

clusteringimmunooncologysinglecellsoftwareclassificationb-cell-receptorbioinformaticsimmunoinformaticsimmunologyquantitative-methodsrep-seqrepertoire-analysist-cell-receptorcpp

5.94 score 2 stars 2 scripts 142 downloads

spatialDE - R wrapper for SpatialDE

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

Last updated 2 months ago

softwaretranscriptomicspythonspatial-datawrapper

5.94 score 3 stars 16 scripts 204 downloads

ResidualMatrix - Creating a DelayedMatrix of Regression Residuals

Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.

Last updated 2 months ago

softwaredatarepresentationregressionbatcheffectexperimentaldesign

5.92 score 1 stars 8 dependents 6 scripts 5.8k downloads

SCOPE - A normalization and copy number estimation method for single-cell DNA sequencing

Whole genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy number profiles at the cellular level. This circumvents the averaging effects associated with bulk-tissue sequencing and has increased resolution yet decreased ambiguity in deconvolving cancer subclones and elucidating cancer evolutionary history. ScDNA-seq data is, however, sparse, noisy, and highly variable even within a homogeneous cell population, due to the biases and artifacts that are introduced during the library preparation and sequencing procedure. Here, we propose SCOPE, a normalization and copy number estimation method for scDNA-seq data. The distinguishing features of SCOPE include: (i) utilization of cell-specific Gini coefficients for quality controls and for identification of normal/diploid cells, which are further used as negative control samples in a Poisson latent factor model for normalization; (ii) modeling of GC content bias using an expectation-maximization algorithm embedded in the Poisson generalized linear models, which accounts for the different copy number states along the genome; (iii) a cross-sample iterative segmentation procedure to identify breakpoints that are shared across cells from the same genetic background.

Last updated 2 months ago

singlecellnormalizationcopynumbervariationsequencingwholegenomecoveragealignmentqualitycontroldataimportdnaseq

5.91 score 81 scripts 212 downloads

MetMashR - Metabolite Mashing with R

A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.

Last updated 2 months ago

workflowstepmetabolomicskegg

5.90 score 2 stars 5 scripts

tidyCoverage - Extract and aggregate genomic coverage over features of interest

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

Last updated 2 months ago

softwaresequencingcoverage

5.90 score 20 stars 6 scripts 116 downloads

MuData - Serialization for MultiAssayExperiment Objects

Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.

Last updated 2 months ago

dataimportanndatabioconductormudatamulti-omicsmultimodal-omicsscrna-seq

5.89 score 5 stars 26 scripts 161 downloads

qsmooth - Smooth quantile normalization

Smooth quantile normalization is a generalization of quantile normalization, which is average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.

Last updated 2 months ago

normalizationpreprocessingmultiplecomparisonmicroarraysequencingrnaseqbatcheffect

5.88 score 1 dependents 84 scripts 354 downloads

MungeSumstats - Standardise summary statistics from GWAS

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

Last updated 4 days ago

snpwholegenomegeneticscomparativegenomicsgenomewideassociationgenomicvariationpreprocessing

5.87 score 1 stars 91 scripts 1.5k downloads

DFplyr - A `DataFrame` (`S4Vectors`) backend for `dplyr`

Provides `dplyr` verbs (`mutate`, `select`, `filter`, etc...) supporting `S4Vectors::DataFrame` objects. Importantly, this is achieved without conversion to an intermediate `tibble`. Adds grouping infrastructure to `DataFrame` which is respected by the transformation verbs.

Last updated 2 months ago

datarepresentationinfrastructuresoftware

5.87 score 21 stars 5 scripts 41 downloads

CNVRanger - Summarization and expression/phenotype association of CNV ranges

The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.

Last updated 2 months ago

copynumbervariationdifferentialexpressiongeneexpressiongenomewideassociationgenomicvariationmicroarrayrnaseqsnpbioconductor-package

5.87 score 7 stars 9 scripts 212 downloads

ggtreeSpace - Visualizing Phylomorphospaces using 'ggtree'

This package is a comprehensive visualization tool specifically designed for exploring phylomorphospace. It not only simplifies the process of generating phylomorphospace, but also enhances it with the capability to add graphic layers to the plot with grammar of graphics to create fully annotated phylomorphospaces. It also provide some utilities to help interpret evolutionary patterns.

Last updated 2 months ago

annotationvisualizationphylogeneticssoftware

5.86 score 5 stars 12 scripts 134 downloads

DiscoRhythm - Interactive Workflow for Discovering Rhythmicity in Biological Data

Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.

Last updated 2 months ago

softwaretimecoursequalitycontrolvisualizationguiprincipalcomponentbioconductordata-visualizationoscillationsrhythm-detectionwebapp

5.86 score 12 stars 9 scripts 180 downloads

crisprBowtie - Bowtie-based alignment of CRISPR gRNA spacer sequences

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.

Last updated 2 months ago

crisprfunctionalgenomicsalignmentalignerbioconductorbioconductor-packagebowtiecrispr-analysiscrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequencessgrnasgrna-design

5.86 score 3 stars 4 dependents 7 scripts 297 downloads

ChromSCape - Analysis of single-cell epigenomics datasets with a Shiny App

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

Last updated 2 months ago

shinyappssoftwaresinglecellchipseqatacseqmethylseqclassificationclusteringepigeneticsprincipalcomponentannotationbatcheffectmultiplecomparisonnormalizationpathwayspreprocessingqualitycontrolreportwritingvisualizationgenesetenrichmentdifferentialpeakcallingepigenomicsshinysingle-cellcpp

5.85 score 14 stars 17 scripts 180 downloads

demuxmix - Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models

A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.

Last updated 2 months ago

singlecellsequencingpreprocessingclassificationregression

5.84 score 4 stars 1 dependents 19 scripts 354 downloads

cfDNAPro - cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization.

Last updated 2 months ago

visualizationsequencingwholegenomebioinformaticscancer-genomicscancer-researchcell-free-dnaearly-detectiongenomics-visualizationliquid-biopsyswgswhole-genome-sequencing

5.83 score 28 stars 12 scripts 188 downloads

scBubbletree - Quantitative visual exploration of scRNA-seq data

scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation.

Last updated 2 months ago

visualizationclusteringsinglecelltranscriptomicsrnaseqbig-databigdatascrna-seqscrna-seq-analysisvisualvisual-exploration

5.82 score 6 stars 8 scripts 154 downloads

CCPlotR - Plots For Visualising Cell-Cell Interactions

CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc.

Last updated 2 months ago

singlecellnetworkvisualizationcellbiologysystemsbiology

5.79 score 41 stars 7 scripts 140 downloads

SingleCellSignalR - Cell Signalling Using Single Cell RNAseq Data Analysis

Allows single cell RNA seq data analysis, clustering, creates internal network and infers cell-cell interactions.

Last updated 2 months ago

singlecellnetworkclusteringrnaseqclassification

5.78 score 1 dependents 29 scripts 438 downloads

ompBAM - C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files

This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.

Last updated 2 months ago

alignmentdataimportrnaseqsoftwaresequencingtranscriptomicssinglecell

5.78 score 4 stars 1 dependents 2 scripts 194 downloads

deconvR - Simulation and Deconvolution of Omic Profiles

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

Last updated 2 months ago

dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics

5.78 score 10 stars 15 scripts 270 downloads

circRNAprofiler - circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.

Last updated 2 months ago

annotationstructuralpredictionfunctionalpredictiongenepredictiongenomeassemblydifferentialexpression

5.78 score 10 stars 5 scripts 288 downloads

GeDi - Defining and visualizing the distances between different genesets

The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.

Last updated 2 months ago

guigenesetenrichmentsoftwaretranscriptionrnaseqvisualizationclusteringpathwaysreportwritinggokeggreactomeshinyapps

5.77 score 1 stars 22 scripts 182 downloads

SpaNorm - Spatially-aware normalisation for spatial transcriptomics data

This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.

Last updated 2 months ago

softwaregeneexpressiontranscriptomicsspatialcellbiology

5.77 score 9 stars 3 scripts

alabaster.sce - Load and Save SingleCellExperiment from File

Save SingleCellExperiment into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 2 months ago

dataimportdatarepresentation

5.76 score 3 dependents 4 scripts 1.4k downloads

iSEEtree - Interactive visualisation for microbiome data

iSEEtree is an extension of iSEE for the TreeSummarizedExperiment. It leverages the functionality from the miaViz package for microbiome data visualisation to create panels that are specific for TreeSummarizedExperiment objects. Not surprisingly, it also depends on the generic panels from iSEE.

Last updated 2 months ago

microbiomesoftwarevisualizationguishinyappsdataimportshiny-appsvisualisation

5.76 score 3 stars 5 scripts 166 downloads

BANDITS - BANDITS: Bayesian ANalysis of DIfferenTial Splicing

BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.

Last updated 2 months ago

differentialsplicingalternativesplicingbayesiangeneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationopenblascpp

5.75 score 17 stars 1 dependents 11 scripts 338 downloads

APAlyzer - A toolkit for APA analysis using RNA-seq data

Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.

Last updated 2 months ago

sequencingrnaseqdifferentialexpressiongeneexpressiongeneregulationannotationdataimportsoftwareative-polyadenylationbioinformatics-toolrna-seq

5.75 score 7 stars 9 scripts 188 downloads

MsBackendMassbank - Mass Spectrometry Data Backend for MassBank record Files

Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.

Last updated 2 months ago

infrastructuremassspectrometrymetabolomicsdataimportmassbankspectra

5.74 score 3 stars 23 scripts 210 downloads

HybridExpress - Comparative analysis of RNA-seq data for hybrids and their progenitors

HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature.

Last updated 2 months ago

softwarefunctionalgenomicsgeneexpressiontranscriptomicsrnaseqclassificationdifferentialexpressiongene-expressionhybridpolyploidyrna-seq

5.73 score 12 stars 2 scripts 179 downloads

iSEEindex - iSEE extension for a landing page to a custom collection of data sets

This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.

Last updated 2 months ago

softwareinfrastructurebioconductorhacktoberfest

5.73 score 2 stars 8 scripts 121 downloads

atSNP - Affinity test for identifying regulatory SNPs

atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.

Last updated 2 months ago

softwarechipseqgenomeannotationmotifannotationvisualizationcpp

5.73 score 1 stars 36 scripts 328 downloads

GenomicPlot - Plot profiles of next generation sequencing data in genomic features

Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. 'GenomicPlot' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.

Last updated 2 days ago

alternativesplicingchipseqcoveragegeneexpressionrnaseqsequencingsoftwaretranscriptionvisualizationannotation

5.71 score 3 stars 4 scripts 170 downloads

CoSIA - An Investigation Across Different Species and Tissues

Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison.

Last updated 2 months ago

softwarebiologicalquestiongeneexpressionmultiplecomparisonthirdpartyclientdataimportgui

5.70 score 5 stars 3 scripts 67 downloads

DAMEfinder - Finds DAMEs - Differential Allelicly MEthylated regions

'DAMEfinder' offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.

Last updated 2 months ago

dnamethylationdifferentialmethylationcoverage

5.70 score 10 stars 9 scripts 257 downloads

PAST - Pathway Association Study Tool (PAST)

PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.

Last updated 2 months ago

pathwaysgenesetenrichment

5.70 score 5 stars 7 scripts 162 downloads

CTdata - Data companion to CTexploreR

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

Last updated 2 months ago

transcriptomicsepigeneticsgeneexpressiondataimportexperimenthubsoftware

5.69 score 1 stars 1 dependents 1 scripts 117 downloads

scviR - experimental inferface from R to scvi-tools

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

Last updated 2 months ago

infrastructuresinglecelldataimportbioconductorcite-seqscverse

5.69 score 6 stars 11 scripts 124 downloads

GWENA - Pipeline for augmented co-expression analysis

The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.

Last updated 2 months ago

softwaregeneexpressionnetworkclusteringgraphandnetworkgenesetenrichmentpathwaysvisualizationrnaseqtranscriptomicsmrnamicroarraymicroarraynetworkenrichmentsequencinggoco-expressionenrichment-analysisgenenetwork-analysispipeline

5.68 score 22 stars 11 scripts 458 downloads

CytoGLMM - Conditional Differential Analysis for Flow and Mass Cytometry Experiments

The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.

Last updated 2 months ago

flowcytometryproteomicssinglecellcellbasedassayscellbiologyimmunooncologyregressionstatisticalmethodsoftware

5.68 score 2 stars 1 dependents 1 scripts 178 downloads

ReactomeContentService4R - Interface for the Reactome Content Service

Reactome is a free, open-source, open access, curated and peer-reviewed knowledgebase of bio-molecular pathways. This package is to interact with the Reactome Content Service API. Pre-built functions would allow users to retrieve data and images that consist of proteins, pathways, and other molecules related to a specific gene or entity in Reactome.

Last updated 2 months ago

dataimportpathwaysreactome

5.68 score 4 stars 1 dependents 9 scripts 226 downloads

enrichViewNet - From functional enrichment results to biological networks

This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.

Last updated 2 months ago

biologicalquestionsoftwarenetworknetworkenrichmentgocystocapefunctional-enrichment

5.68 score 5 stars 6 scripts 141 downloads

rgoslin - Lipid Shorthand Name Parsing and Normalization

The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.

Last updated 2 months ago

softwarelipidomicsmetabolomicspreprocessingnormalizationmassspectrometrycpp

5.66 score 5 stars 23 scripts 219 downloads

debCAM - Deconvolution by Convex Analysis of Mixtures

An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.

Last updated 2 months ago

softwarecellbiologygeneexpressionopenjdk

5.66 score 7 stars 13 scripts 272 downloads

DIAlignR - Dynamic Programming Based Alignment of MS2 Chromatograms

To obtain unbiased proteome coverage from a biological sample, mass-spectrometer is operated in Data Independent Acquisition (DIA) mode. Alignment of these DIA runs establishes consistency and less missing values in complete data-matrix. This package implements dynamic programming with affine gap penalty based approach for pair-wise alignment of analytes. A hybrid approach of global alignment (through MS2 features) and local alignment (with MS2 chromatograms) is implemented in this tool.

Last updated 5 days ago

massspectrometrymetabolomicsproteomicsalignmentsoftwarecpp

5.65 score 5 stars 10 scripts 147 downloads

metabCombiner - Method for Combining LC-MS Metabolomics Feature Measurements

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

Last updated 2 months ago

softwaremassspectrometrymetabolomicsmass-spectrometry

5.65 score 10 stars 5 scripts 202 downloads

ppcseq - Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models

Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq to analyse several publicly available datasets using popular tools, we show that from 3 to 10 percent of differentially abundant transcripts across algorithms and datasets had statistics inflated by the presence of outliers.

Last updated 2 months ago

rnaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsbayesian-inferencedeseq2edgernegative-binomialoutlierstancpp

5.65 score 7 stars 16 scripts 179 downloads

planet - Placental DNA methylation analysis tools

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

Last updated 2 months ago

softwaredifferentialmethylationepigeneticsmicroarraymethylationarraydnamethylationcpgislandancestrydna-methylation-datageneticsinferencemachine-learningplacenta

5.64 score 4 stars 1 dependents 12 scripts 318 downloads

crossmeta - Cross Platform Meta-Analysis of Microarray Data

Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. The user then selects control and treatment samples in order to perform differential expression analyses for all comparisons. After analysing each contrast seperately, the user can select tissue sources for each contrast and specify any tissue sources that should be grouped for the subsequent meta-analyses.

Last updated 5 days ago

geneexpressiontranscriptiondifferentialexpressionmicroarraytissuemicroarrayonechannelannotationbatcheffectpreprocessinggui

5.63 score 3 stars 19 scripts 266 downloads

SEtools - SEtools: tools for working with SummarizedExperiment

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

Last updated 2 months ago

geneexpression

5.63 score 2 stars 71 scripts 412 downloads

flowcatchR - Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.

Last updated 2 days ago

softwarevisualizationcellbiologyclassificationinfrastructureguishinyappsbioconductorfluorescencemicroscopyparticlestracking

5.62 score 4 stars 8 scripts 241 downloads

TMSig - Tools for Molecular Signatures

The TMSig package contains tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene or kinase sets). It includes fast, memory efficient functions to construct sparse incidence and similarity matrices and filter, cluster, invert, and decompose sets. Additionally, bubble heatmaps can be created to visualize the results of any differential or molecular signatures analysis.

Last updated 2 months ago

clusteringgenesetenrichmentgraphandnetworkpathwaysvisualizationgene-setsmolecular-signatures

5.62 score 4 stars 4 scripts

AnVILAz - R / Bioconductor Support for the AnVIL Azure Platform

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources.

Last updated 2 months ago

softwareinfrastructurethirdpartyclient

5.62 score 5 scripts 102 downloads

methyLImp2 - Missing value estimation of DNA methylation data

This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.

Last updated 2 months ago

dnamethylationmicroarraysoftwaremethylationarrayregressionimputationmethylationmissing-value-imputation

5.62 score 6 stars 3 scripts 126 downloads

cytoviewer - An interactive multi-channel image viewer for R

This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.

Last updated 2 months ago

immunooncologysoftwaresinglecellonechanneltwochannelmultichannelspatialdataimportbioconductorimagingshinyvisualization

5.61 score 6 stars 15 scripts 209 downloads

gpuMagic - An openCL compiler with the capacity to compile R functions and run the code on GPU

The package aims to help users write openCL code with little or no effort. It is able to compile an user-defined R function and run it on a device such as a CPU or a GPU. The user can also write and run their openCL code directly by calling .kernel function.

Last updated 2 months ago

infrastructureocl-icdcpp

5.60 score 10 stars 1 scripts 184 downloads

demuxSNP - scRNAseq demultiplexing using cell hashing and SNPs

This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework.

Last updated 2 months ago

classificationsinglecell

5.60 score 6 stars 22 scripts 116 downloads

Pedixplorer - Pedigree Functions

Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

Last updated 2 months ago

softwaredatarepresentationgeneticsgraphandnetworkvisualizationpedigree

5.57 score 1 stars 10 scripts 121 downloads

limpca - An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods

This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.

Last updated 2 months ago

statisticalmethodprincipalcomponentregressionvisualizationexperimentaldesignmultiplecomparisongeneexpressionmetabolomics

5.56 score 1 stars 2 scripts 98 downloads

Damsel - Damsel: an end to end analysis of DamID

Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.

Last updated 2 months ago

differentialmethylationpeakdetectiongenepredictiongenesetenrichment

5.56 score 20 scripts 141 downloads

MSstatsLiP - LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

Last updated 2 months ago

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolcpp

5.56 score 6 stars 5 scripts 190 downloads

TAPseq - Targeted scRNA-seq primer design for TAP-seq

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.

Last updated 2 months ago

singlecellsequencingtechnologycrisprpooledscreens

5.56 score 4 stars 9 scripts 194 downloads

BgeeCall - Automatic RNA-Seq present/absent gene expression calls generation

BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).

Last updated 2 months ago

softwaregeneexpressionrnaseqbiologygene-expressiongene-levelintergenic-regionspresent-absent-callsrna-seqrna-seq-librariesscrna-seq

5.56 score 3 stars 9 scripts 185 downloads

HiLDA - Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

A package built under the Bayesian framework of applying hierarchical latent Dirichlet allocation. It statistically tests whether the mutational exposures of mutational signatures (Shiraishi-model signatures) are different between two groups. The package also provides inference and visualization.

Last updated 2 months ago

softwaresomaticmutationsequencingstatisticalmethodbayesianmutational-signaturesrjagssomatic-mutationscppjags

5.56 score 3 stars 1 dependents 7 scripts 184 downloads

QSutils - Quasispecies Diversity

Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.

Last updated 2 months ago

softwaregeneticsdnaseqgeneticvariabilitysequencingalignmentsequencematchingdataimport

5.56 score 1 dependents 8 scripts 289 downloads

lionessR - Modeling networks for individual samples using LIONESS

LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks.

Last updated 2 months ago

networknetworkinferencegeneexpression

5.55 score 21 stars 17 scripts 156 downloads

PLSDAbatch - PLSDA-batch

A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings.

Last updated 2 months ago

statisticalmethoddimensionreductionprincipalcomponentclassificationmicrobiomebatcheffectnormalizationvisualization

5.55 score 13 stars 18 scripts 133 downloads

dar - Differential Abundance Analysis by Consensus

Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error that are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness. With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way.

Last updated 2 months ago

softwaresequencingmicrobiomemetagenomicsmultiplecomparisonnormalizationbioconductorbiomarker-discoverydifferential-abundance-analysisfeature-selectionmicrobiologyphyloseq

5.54 score 1 stars 8 scripts 122 downloads

MsQuality - MsQuality - Quality metric calculation from Spectra and MsExperiment objects

The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

Last updated 2 months ago

metabolomicsproteomicsmassspectrometryqualitycontrolmass-spectrometryqc

5.54 score 7 stars 2 scripts 158 downloads

Rcwl - An R interface to the Common Workflow Language

The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines.

Last updated 2 months ago

softwareworkflowstepimmunooncology

5.52 score 2 dependents 37 scripts 202 downloads

GeoDiff - Count model based differential expression and normalization on GeoMx RNA data

A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette.

Last updated 2 months ago

geneexpressiondifferentialexpressionnormalizationopenblascppopenmp

5.51 score 8 stars 9 scripts 184 downloads

cbpManager - Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics

This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.

Last updated 2 months ago

immunooncologydataimportdatarepresentationguithirdpartyclientpreprocessingvisualizationcancer-genomicscbioportalclinical-datafilegeneratormutation-datapatient-data

5.51 score 8 stars 1 scripts 154 downloads

rprimer - Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.

Last updated 2 months ago

alignmentddpcrcoveragemultiplesequencealignmentsequencematchingqpcr

5.49 score 4 stars 13 scripts 161 downloads

GRaNIE - GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.

Last updated 2 months ago

softwaregeneexpressiongeneregulationnetworkinferencegenesetenrichmentbiomedicalinformaticsgeneticstranscriptomicsatacseqrnaseqgraphandnetworkregressiontranscriptionchipseq

5.49 score 23 scripts 226 downloads

TDbasedUFE - Tensor Decomposition Based Unsupervised Feature Extraction

This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also potentially applicable to single cell omics data sets.

Last updated 2 months ago

geneexpressionfeatureextractionmethylationarraysinglecellbioinformaticsdna-methylationgene-expression-profileshistone-modificationsmultiomicstensor-decomposition

5.48 score 5 stars 1 dependents 9 scripts 142 downloads

katdetectr - Detection, Characterization and Visualization of Kataegis in Sequencing Data

Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.

Last updated 2 months ago

wholegenomesoftwaresnpsequencingclassificationvariantannotation

5.48 score 5 stars 4 scripts 170 downloads

tripr - T-cell Receptor/Immunoglobulin Profiler (TRIP)

TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.

Last updated 2 months ago

batcheffectmultiplecomparisongeneexpressionimmunooncologytargetedresequencingbioconductorclonotype

5.48 score 2 stars 4 scripts 136 downloads

UMI4Cats - UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.

Last updated 2 months ago

qualitycontrolpreprocessingalignmentnormalizationvisualizationsequencingcoveragechromatinchromatin-interactiongenomicsumi4c

5.48 score 5 stars 7 scripts 158 downloads

DEWSeq - Differential Expressed Windows Based on Negative Binomial Distribution

DEWSeq is a sliding window approach for the analysis of differentially enriched binding regions eCLIP or iCLIP next generation sequencing data.

Last updated 2 months ago

sequencinggeneregulationfunctionalgenomicsdifferentialexpressionbioinformaticseclipngs-analysis

5.48 score 5 stars 4 scripts 154 downloads

INTACT - Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis

This package integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.

Last updated 2 months ago

bayesiangenesetenrichment

5.47 score 14 stars 14 scripts 106 downloads

mobileRNA - mobileRNA: Investigate the RNA mobilome & population-scale changes

Genomic analysis can be utilised to identify differences between RNA populations in two conditions, both in production and abundance. This includes the identification of RNAs produced by multiple genomes within a biological system. For example, RNA produced by pathogens within a host or mobile RNAs in plant graft systems. The mobileRNA package provides methods to pre-process, analyse and visualise the sRNA and mRNA populations based on the premise of mapping reads to all genotypes at the same time.

Last updated 2 months ago

visualizationrnaseqsequencingsmallrnagenomeassemblyclusteringexperimentaldesignqualitycontrolworkflowstepalignmentpreprocessingbioinformaticsplant-science

5.45 score 4 stars 2 scripts 140 downloads

metagene2 - A package to produce metagene plots

This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.

Last updated 2 months ago

chipseqgeneticsmultiplecomparisoncoveragealignmentsequencing

5.45 score 4 stars 10 scripts 180 downloads

scrapper - Bindings to C++ Libraries for Single-Cell Analysis

Implements R bindings to C++ code for analyzing single-cell (expression) data, mostly from various libscran libraries. Each function performs an individual step in the single-cell analysis workflow, ranging from quality control to clustering and marker detection. It is mostly intended for other Bioconductor package developers to build more user-friendly end-to-end workflows.

Last updated 9 hours ago

normalizationrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectqualitycontroldifferentialexpressionfeatureextractionprincipalcomponentclusteringcpp

5.42 score 29 scripts 125 downloads

sketchR - An R interface for python subsampling/sketching algorithms

Provides an R interface for various subsampling algorithms implemented in python packages. Currently, interfaces to the geosketch and scSampler python packages are implemented. In addition it also provides diagnostic plots to evaluate the subsampling.

Last updated 10 hours ago

singlecell

5.41 score 2 stars 3 scripts 168 downloads

gINTomics - Multi-Omics data integration

gINTomics is an R package for Multi-Omics data integration and visualization. gINTomics is designed to detect the association between the expression of a target and of its regulators, taking into account also their genomics modifications such as Copy Number Variations (CNV) and methylation. What is more, gINTomics allows integration results visualization via a Shiny-based interactive app.

Last updated 2 months ago

geneexpressionrnaseqmicroarrayvisualizationcopynumbervariationgenetarget

5.41 score 3 stars 3 scripts 76 downloads

CardinalIO - Read and write mass spectrometry imaging files

Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.

Last updated 2 months ago

softwareinfrastructuredataimportmassspectrometryimagingmassspectrometrycpp

5.41 score 1 stars 1 dependents 3 scripts 278 downloads

TEKRABber - An R package estimates the correlations of orthologs and transposable elements between two species

TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.

Last updated 2 months ago

differentialexpressionnormalizationtranscriptiongeneexpressionbioconductorcpp

5.40 score 3 stars 14 scripts 357 downloads

IsoBayes - IsoBayes: Single Isoform protein inference Method via Bayesian Analyses

IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.

Last updated 2 months ago

statisticalmethodbayesianproteomicsmassspectrometryalternativesplicingsequencingrnaseqgeneexpressiongeneticsvisualizationsoftwarecpp

5.39 score 7 stars 10 scripts 170 downloads

lute - Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments

Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.

Last updated 2 months ago

rnaseqsequencingsinglecellcoveragetranscriptomicsnormalization

5.38 score 2 stars 3 scripts 104 downloads

ReUseData - Reusable and reproducible Data Management

ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()".

Last updated 2 months ago

softwareinfrastructuredataimportpreprocessingimmunooncology

5.38 score 4 stars 7 scripts 169 downloads

speckle - Statistical methods for analysing single cell RNA-seq data

The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.

Last updated 2 months ago

singlecellrnaseqregressiongeneexpression

5.38 score 240 scripts 344 downloads

iSEEhub - iSEE for the Bioconductor ExperimentHub

This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.

Last updated 2 months ago

dataimportimmunooncology infrastructureshinyappssinglecellsoftwarebioconductorbioconductor-packagehacktoberfestisee

5.38 score 3 stars 4 scripts 357 downloads

iSEEhex - iSEE extension for summarising data points in hexagonal bins

This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package.

Last updated 2 months ago

softwareinfrastructurebioconductoriseeushiny-r

5.38 score 2 dependents 7 scripts 220 downloads

fastreeR - Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.

Last updated 2 months ago

phylogeneticsmetagenomicsclustering

5.38 score 3 stars 20 scripts 186 downloads

beer - Bayesian Enrichment Estimation in R

BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.

Last updated 2 months ago

softwarestatisticalmethodbayesiansequencingcoveragejagscpp

5.38 score 10 stars 12 scripts 152 downloads

diffUTR - diffUTR: Streamlining differential exon and 3' UTR usage

The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases.

Last updated 2 months ago

geneexpression

5.38 score 6 stars 9 scripts 162 downloads

DepecheR - Determination of essential phenotypic elements of clusters in high-dimensional entities

The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.

Last updated 2 months ago

softwarecellbasedassaystranscriptiondifferentialexpressiondatarepresentationimmunooncologytranscriptomicsclassificationclusteringdimensionreductionfeatureextractionflowcytometryrnaseqsinglecellvisualizationcpp

5.38 score 15 scripts 334 downloads

rScudo - Signature-based Clustering for Diagnostic Purposes

SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.

Last updated 2 months ago

geneexpressiondifferentialexpressionbiomedicalinformaticsclassificationclusteringgraphandnetworknetworkproteomicstranscriptomicssystemsbiologyfeatureextraction

5.37 score 3 stars 13 scripts 164 downloads

BumpyMatrix - Bumpy Matrix of Non-Scalar Objects

Implements the BumpyMatrix class and several subclasses for holding non-scalar objects in each entry of the matrix. This is akin to a ragged array but the raggedness is in the third dimension, much like a bumpy surface - hence the name. Of particular interest is the BumpyDataFrameMatrix, where each entry is a Bioconductor data frame. This allows us to naturally represent multivariate data in a format that is compatible with two-dimensional containers like the SummarizedExperiment and MultiAssayExperiment objects.

Last updated 2 months ago

softwareinfrastructuredatarepresentation

5.36 score 1 stars 11 dependents 35 scripts 805 downloads

DifferentialRegulation - Differentially regulated genes from scRNA-seq data

DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) 'ambiguous' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).

Last updated 2 months ago

differentialsplicingbayesiangeneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationsinglecellgenetargetopenblascpp

5.35 score 9 stars 4 scripts 170 downloads

RolDE - RolDE: Robust longitudinal Differential Expression

RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings.

Last updated 2 months ago

statisticalmethodsoftwaretimecourseregressionproteomicsdifferentialexpression

5.35 score 5 stars 1 scripts 140 downloads

svaNUMT - NUMT detection from structural variant calls

svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.

Last updated 2 months ago

dataimportsequencingannotationgeneticsvariantannotation

5.35 score 3 stars 6 scripts 162 downloads

tRNAdbImport - Importing from tRNAdb and mitotRNAdb as GRanges objects

tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (http://trna.bioinf.uni-leipzig.de) as GRanges object.

Last updated 2 months ago

softwarevisualizationdataimportbioconductorsequencesstructurestrnatrna-genestrna-sequencestrnadb

5.35 score 1 stars 1 dependents 3 scripts 342 downloads

MOSClip - Multi Omics Survival Clip

Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.

Last updated 2 months ago

softwarestatisticalmethodgraphandnetworksurvivalregressiondimensionreductionpathwaysreactome

5.34 score 5 scripts 41 downloads

scReClassify - scReClassify: post hoc cell type classification of single-cell RNA-seq data

A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.

Last updated 2 months ago

softwaretranscriptomicssinglecellclassificationsupportvectormachine

5.34 score 10 stars 11 scripts 158 downloads

sRACIPE - Systems biology tool to simulate gene regulatory circuits

sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.

Last updated 2 months ago

researchfieldsystemsbiologymathematicalbiologygeneexpressiongeneregulationgenetargetcppgenegene-circuit-explorergeneticsraciperegulatory-networkssimulated-annealingsimulationsracipestochasticcpp

5.33 score 215 scripts 170 downloads

VDJdive - Analysis Tools for 10X V(D)J Data

This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.

Last updated 2 months ago

softwareimmunooncologysinglecellannotationrnaseqtargetedresequencingcpp

5.32 score 7 stars 1 scripts 136 downloads

GEOexplorer - GEOexplorer: a webserver for gene expression analysis and visualisation

GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).

Last updated 2 months ago

softwaregeneexpressionmrnamicroarraydifferentialexpressionmicroarraymicrornaarraytranscriptomicsrnaseq

5.32 score 5 stars 14 scripts 152 downloads

fedup - Fisher's Test for Enrichment and Depletion of User-Defined Pathways

An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.

Last updated 2 months ago

genesetenrichmentpathwaysnetworkenrichmentnetworkbioconductorenrichment

5.32 score 7 stars 10 scripts 137 downloads

funOmics - Aggregating Omics Data into Higher-Level Functional Representations

The 'funOmics' package ggregates or summarizes omics data into higher level functional representations such as GO terms gene sets or KEGG metabolic pathways. The aggregated data matrix represents functional activity scores that facilitate the analysis of functional molecular sets while allowing to reduce dimensionality and provide easier and faster biological interpretations. Coordinated functional activity scores can be as informative as single molecules!

Last updated 2 months ago

softwaretranscriptomicsmetabolomicsproteomicspathwaysgokegg

5.30 score 5 stars 3 scripts 108 downloads

CDI - Clustering Deviation Index (CDI)

Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.

Last updated 2 months ago

singlecellsoftwareclusteringvisualizationsequencingrnaseqcellbasedassays

5.30 score 5 stars 4 scripts 113 downloads

RnaSeqSampleSize - RnaSeqSampleSize

RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data. It controls FDR for multiple testing and utilizes the average read count and dispersion distributions from real data to estimate a more reliable sample size. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization.

Last updated 2 months ago

immunooncologyexperimentaldesignsequencingrnaseqgeneexpressiondifferentialexpressioncpp

5.30 score 20 scripts 266 downloads

scCB2 - CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.

Last updated 2 months ago

dataimportrnaseqsinglecellsequencinggeneexpressiontranscriptomicspreprocessingclustering

5.30 score 10 stars 5 scripts 151 downloads

MEAT - Muscle Epigenetic Age Test

This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC).

Last updated 2 months ago

epigeneticsdnamethylationmicroarraynormalizationbiomedicalinformaticsmethylationarraypreprocessing

5.30 score 4 scripts 152 downloads

preciseTAD - preciseTAD: A machine learning framework for precise TAD boundary prediction

preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution. As an input, it takes BED-formatted genomic coordinates of domain boundaries detected from low-resolution Hi-C data, and coordinates of high-resolution genomic annotations from ENCODE or other consortia. preciseTAD employs several feature engineering strategies and resampling techniques to address class imbalance, and trains an optimized random forest model for predicting low-resolution domain boundaries. Translated on a base-level, preciseTAD predicts the probability for each base to be a boundary. Density-based clustering and scalable partitioning techniques are used to detect precise boundary regions and summit points. Compared with low-resolution boundaries, preciseTAD boundaries are highly enriched for CTCF, RAD21, SMC3, and ZNF143 signal and more conserved across cell lines. The pre-trained model can accurately predict boundaries in another cell line using CTCF, RAD21, SMC3, and ZNF143 annotation data for this cell line.

Last updated 2 months ago

softwarehicsequencingclusteringclassificationfunctionalgenomicsfeatureextraction

5.29 score 7 stars 14 scripts 155 downloads

DeMixT - Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.

Last updated 2 months ago

softwarestatisticalmethodclassificationgeneexpressionsequencingmicroarraytissuemicroarraycoveragecppopenmp

5.27 score 25 scripts 218 downloads

SingleCellAlleleExperiment - S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes

Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.

Last updated 2 days ago

datarepresentationinfrastructuresinglecelltranscriptomicsgeneexpressiongeneticsimmunooncologydataimport

5.27 score 6 stars 12 scripts 165 downloads

MultiRNAflow - An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions

Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

Last updated 2 months ago

sequencingrnaseqgeneexpressiontranscriptiontimecoursepreprocessingvisualizationnormalizationprincipalcomponentclusteringdifferentialexpressiongenesetenrichmentpathways

5.26 score 6 stars 4 scripts 136 downloads

adverSCarial - adverSCarial, generate and analyze the vulnerability of scRNA-seq classifier to adversarial attacks

adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single-gene attack involves making a small modification to the input to alter the classification. The max-change attack involves making a large modification to the input without changing its classification. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks.

Last updated 2 months ago

softwaresinglecelltranscriptomicsclassification

5.26 score 10 scripts 120 downloads

cfTools - Informatics Tools for Cell-Free DNA Study

The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

Last updated 2 months ago

softwarebiomedicalinformaticsepigeneticssequencingmethylseqdnamethylationdifferentialmethylationcpp

5.26 score 6 stars 2 scripts 133 downloads

SiPSiC - Calculate Pathway Scores for Each Cell in scRNA-Seq Data

Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells.

Last updated 2 months ago

softwaredifferentialexpressiongenesetenrichmentbiomedicalinformaticscellbiologytranscriptomicsrnaseqsinglecelltranscriptionsequencingimmunooncologydataimport

5.26 score 6 stars 3 scripts 183 downloads

epistack - Heatmaps of Stack Profiles from Epigenetic Signals

The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.

Last updated 2 months ago

rnaseqpreprocessingchipseqgeneexpressioncoveragebioinformatics

5.26 score 6 stars 5 scripts 132 downloads

FindIT2 - find influential TF and Target based on multi-omics data

This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.

Last updated 2 months ago

softwareannotationchipseqatacseqgeneregulationmultiplecomparisongenetarget

5.26 score 6 stars 7 scripts 142 downloads

ReactomeGraph4R - Interface for the Reactome Graph Database

Pathways, reactions, and biological entities in Reactome knowledge are systematically represented as an ordered network. Instances are represented as nodes and relationships between instances as edges; they are all stored in the Reactome Graph Database. This package serves as an interface to query the interconnected data from a local Neo4j database, with the aim of minimizing the usage of Neo4j Cypher queries.

Last updated 2 months ago

dataimportpathwaysreactomenetworkgraphandnetwork

5.26 score 6 stars 6 scripts 115 downloads

periodicDNA - Set of tools to identify periodic occurrences of k-mers in DNA sequences

This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.

Last updated 2 months ago

sequencematchingmotifdiscoverymotifannotationsequencingcoveragealignmentdataimport

5.26 score 6 stars 5 scripts 146 downloads

EnMCB - Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Creation of the correlated blocks using DNA methylation profiles. Machine learning models can be constructed to predict differentially methylated blocks and disease progression.

Last updated 2 months ago

normalizationdnamethylationmethylationarraysupportvectormachine

5.26 score 9 stars 2 scripts 177 downloads

NPARC - Non-parametric analysis of response curves for thermal proteome profiling experiments

Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

Last updated 2 months ago

softwareproteomics

5.26 score 30 scripts 212 downloads

DelayedDataFrame - Delayed operation on DataFrame using standard DataFrame metaphor

Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked.

Last updated 2 months ago

infrastructuredatarepresentation

5.26 score 2 stars 1 dependents 3 scripts 174 downloads

SpectraQL - MassQL support for Spectra

The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is inspired by SQL and is by design programming language agnostic. The SpectraQL package adds support for the MassQL query language to R, in particular to MS data represented by Spectra objects. Users can thus apply MassQL expressions to analyze and retrieve specific data from Spectra objects.

Last updated 2 months ago

infrastructureproteomicsmassspectrometrymetabolomics

5.24 score 7 stars 2 scripts

cfdnakit - Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).

Last updated 2 months ago

copynumbervariationsequencingwholegenome

5.24 score 7 stars 8 scripts 114 downloads

omXplore - Vizualization tools for 'omics' datasets with R

This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.

Last updated 2 months ago

softwareshinyappsmassspectrometrydatarepresentationguiqualitycontrolprostar2

5.23 score 19 scripts

epimutacions - Robust outlier identification for DNA methylation data

The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

Last updated 2 months ago

dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp

5.23 score 28 scripts 168 downloads

ProteoDisco - Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

Last updated 2 months ago

softwareproteomicsrnaseqsnpsequencingvariantannotationdataimport

5.20 score 4 stars 4 scripts 142 downloads

methylscaper - Visualization of Methylation Data

methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.

Last updated 2 months ago

dnamethylationepigeneticssequencingvisualizationsinglecellnucleosomepositioning

5.20 score 2 stars 3 scripts 190 downloads

SplicingFactory - Splicing Diversity Analysis for Transcriptome Data

The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.

Last updated 2 months ago

transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgini-indexrna-seqshannon-entropysimpson-indexsplicing

5.20 score 4 stars 1 scripts 132 downloads

MSPrep - Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data

Package performs summarization of replicates, filtering by frequency, several different options for imputing missing data, and a variety of options for transforming, batch correcting, and normalizing data.

Last updated 2 months ago

metabolomicsmassspectrometrypreprocessing

5.20 score 10 stars 4 scripts 362 downloads

DegNorm - DegNorm: degradation normalization for RNA-seq data

This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy.

Last updated 2 months ago

rnaseqnormalizationgeneexpressionalignmentcoveragedifferentialexpressionbatcheffectsoftwaresequencingimmunooncologyqualitycontroldataimportopenblascppopenmp

5.20 score 1 stars 3 scripts 165 downloads

scGPS - A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

The package implements two main algorithms to answer two key questions: a SCORE (Stable Clustering at Optimal REsolution) to find subpopulations, followed by scGPS to investigate the relationships between subpopulations.

Last updated 2 months ago

singlecellclusteringdataimportsequencingcoverageopenblascpp

5.20 score 4 stars 7 scripts 201 downloads

scRecover - scRecover for imputation of single-cell RNA-seq data

scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.

Last updated 2 months ago

geneexpressionsinglecellrnaseqtranscriptomicssequencingpreprocessingsoftware

5.20 score 8 stars 9 scripts 160 downloads

sitePath - Phylogeny-based sequence clustering with site polymorphism

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

Last updated 2 months ago

alignmentmultiplesequencealignmentphylogeneticssnpsoftwaremutationcpp

5.20 score 8 stars 9 scripts 166 downloads

DESpace - DESpace: a framework to discover spatially variable genes

Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates.

Last updated 2 months ago

spatialsinglecellrnaseqtranscriptomicsgeneexpressionsequencingdifferentialexpressionstatisticalmethodvisualization

5.19 score 4 stars 13 scripts 134 downloads

methylCC - Estimate the cell composition of whole blood in DNA methylation samples

A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).

Last updated 2 months ago

microarraysequencingdnamethylationmethylationarraymethylseqwholegenome

5.18 score 19 stars 8 scripts 196 downloads

squallms - Speedy quality assurance via lasso labeling for LC-MS data

squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.

Last updated 2 months ago

massspectrometrymetabolomicsproteomicslipidomicsshinyappsclassificationclusteringfeatureextractionprincipalcomponentregressionpreprocessingqualitycontrolvisualization

5.18 score 3 stars 5 scripts 80 downloads

gatom - Finding an Active Metabolic Module in Atom Transition Network

This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

Last updated 2 months ago

geneexpressiondifferentialexpressionpathwaysnetwork

5.18 score 5 stars 8 scripts 127 downloads

gcatest - Genotype Conditional Association TEST

GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait models. This test conditions on the trait, which makes it immune to confounding by unmodeled environmental factors. Population structure is modeled via logistic factors, which are estimated using the `lfa` package.

Last updated 2 months ago

snpdimensionreductionprincipalcomponentgenomewideassociation

5.18 score 5 stars 4 scripts 240 downloads

coMET - coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as lon:g as the data can be translated to genomic level and for any species.

Last updated 2 months ago

softwaredifferentialmethylationvisualizationsequencinggeneticsfunctionalgenomicsmicroarraymethylationarraymethylseqchipseqdnaseqriboseqrnaseqexomeseqdnamethylationgenomewideassociationmotifannotation

5.18 score 15 scripts 200 downloads

spaSim - Spatial point data simulator for tissue images

A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.

Last updated 2 months ago

statisticalmethodspatialbiomedicalinformatics

5.18 score 2 stars 25 scripts 128 downloads

PhIPData - Container for PhIP-Seq Experiments

PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

Last updated 2 months ago

infrastructuredatarepresentationsequencingcoverage

5.18 score 5 stars 1 dependents 6 scripts 174 downloads

CNVfilteR - Identifies false positives of CNV calling tools by using SNV calls

CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.

Last updated 2 months ago

copynumbervariationsequencingdnaseqvisualizationdataimport

5.18 score 5 stars 1 scripts 176 downloads

snapcount - R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).

Last updated 2 months ago

coveragegeneexpressionrnaseqsequencingsoftwaredataimport

5.16 score 3 stars 12 scripts 183 downloads

MotifPeeker - Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.

Last updated 3 days ago

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis

5.15 score 1 stars 6 scripts 8 downloads

PIUMA - Phenotypes Identification Using Mapper from topological data Analysis

The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.

Last updated 2 months ago

clusteringgraphandnetworkdimensionreductionnetworkclassification

5.15 score 4 stars 2 scripts 110 downloads

lineagespot - Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.

Last updated 2 months ago

variantdetectionvariantannotationsequencing

5.15 score 2 stars 4 scripts 140 downloads

ptairMS - Pre-processing PTR-TOF-MS Data

This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a singl<e ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.

Last updated 2 months ago

softwaremassspectrometrypreprocessingmetabolomicspeakdetectionalignmentcpp

5.15 score 7 stars 3 scripts 140 downloads

SANTA - Spatial Analysis of Network Associations

This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode).

Last updated 2 months ago

networknetworkenrichmentclustering

5.15 score 6 scripts 180 downloads

msImpute - Imputation of label-free mass spectrometry peptides

MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low-rank approximation of the underlying data matrix if they are MAR (method = "v2"), by Barycenter approach if missingness is MNAR ("v2-mnar"), or by Peptide Identity Propagation (PIP).

Last updated 2 months ago

massspectrometryproteomicssoftwarelabel-free-proteomicslow-rank-approximation

5.15 score 14 stars 7 scripts 378 downloads

RNAAgeCalc - A multi-tissue transcriptional age calculator

It has been shown that both DNA methylation and RNA transcription are linked to chronological age and age related diseases. Several estimators have been developed to predict human aging from DNA level and RNA level. Most of the human transcriptional age predictor are based on microarray data and limited to only a few tissues. To date, transcriptional studies on aging using RNASeq data from different human tissues is limited. The aim of this package is to provide a tool for across-tissue and tissue-specific transcriptional age calculation based on GTEx RNASeq data.

Last updated 2 months ago

rnaseqgeneexpressionbiological-ageelastic-netgene-expressiongenotype-tissue-expressionpredictionregularized-regressionrna-seq

5.15 score 7 stars 10 scripts 180 downloads

MouseFM - In-silico methods for genetic finemapping in inbred mice

This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%).

Last updated 2 months ago

geneticssnpgenetargetvariantannotationgenomicvariationmultiplecomparisonsystemsbiologymathematicalbiologypatternlogicgenepredictionbiomedicalinformaticsfunctionalgenomicsfinemapgene-candidatesinbred-miceinbred-strainsmouseqtlqtl-mapping

5.13 score 5 scripts 359 downloads

awst - Asymmetric Within-Sample Transformation

We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experimental artifacts.

Last updated 2 months ago

normalizationgeneexpressionrnaseqsoftwaretranscriptomicssequencingsinglecell

5.13 score 3 stars 15 scripts 260 downloads

SGCP - SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks

SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.

Last updated 2 months ago

geneexpressiongenesetenrichmentnetworkenrichmentsystemsbiologyclassificationclusteringdimensionreductiongraphandnetworkneuralnetworknetworkmrnamicroarrayrnaseqvisualizationbioinformaticsgenecoexpressionnetworkgraphsnetworkclusteringnetworksself-trainingsemi-supervised-learningunsupervised-learning

5.12 score 2 stars 44 scripts 245 downloads

densvis - Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction

Implements the density-preserving modification to t-SNE and UMAP described by Narayan et al. (2020) <doi:10.1101/2020.05.12.077776>. The non-linear dimensionality reduction techniques t-SNE and UMAP enable users to summarise complex high-dimensional sequencing data such as single cell RNAseq using lower dimensional representations. These lower dimensional representations enable the visualisation of discrete transcriptional states, as well as continuous trajectory (for example, in early development). However, these methods focus on the local neighbourhood structure of the data. In some cases, this results in misleading visualisations, where the density of cells in the low-dimensional embedding does not represent the transcriptional heterogeneity of data in the original high-dimensional space. den-SNE and densMAP aim to enable more accurate visual interpretation of high-dimensional datasets by producing lower-dimensional embeddings that accurately represent the heterogeneity of the original high-dimensional space, enabling the identification of homogeneous and heterogeneous cell states. This accuracy is accomplished by including in the optimisation process a term which considers the local density of points in the original high-dimensional space. This can help to create visualisations that are more representative of heterogeneity in the original high-dimensional space.

Last updated 2 months ago

dimensionreductionvisualizationsoftwaresinglecellsequencingcppopenmp

5.12 score 2 stars 10 scripts 2.6k downloads

MAGeCKFlute - Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

CRISPR (clustered regularly interspaced short palindrome repeats) coupled with nuclease Cas9 (CRISPR/Cas9) screens represent a promising technology to systematically evaluate gene functions. Data analysis for CRISPR/Cas9 screens is a critical process that includes identifying screen hits and exploring biological functions for these hits in downstream analysis. We have previously developed two algorithms, MAGeCK and MAGeCK-VISPR, to analyze CRISPR/Cas9 screen data in various scenarios. These two algorithms allow users to perform quality control, read count generation and normalization, and calculate beta score to evaluate gene selection performance. In downstream analysis, the biological functional analysis is required for understanding biological functions of these identified genes with different screening purposes. Here, We developed MAGeCKFlute for supporting downstream analysis. MAGeCKFlute provides several strategies to remove potential biases within sgRNA-level read counts and gene-level beta scores. The downstream analysis with the package includes identifying essential, non-essential, and target-associated genes, and performing biological functional category analysis, pathway enrichment analysis and protein complex enrichment analysis of these genes. The package also visualizes genes in multiple ways to benefit users exploring screening data. Collectively, MAGeCKFlute enables accurate identification of essential, non-essential, and targeted genes, as well as their related biological functions. This vignette explains the use of the package and demonstrates typical workflows.

Last updated 5 days ago

functionalgenomicscrisprpooledscreensqualitycontrolnormalizationgenesetenrichmentpathwaysvisualizationgenetargetkegg

5.11 score 1 dependents 57 scripts 740 downloads

gDNAx - Diagnostics for assessing genomic DNA contamination in RNA-seq data

Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.

Last updated 2 months ago

transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomicssplicedalignmentalignment

5.08 score 1 stars 3 scripts 157 downloads

retrofit - RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics

RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.

Last updated 2 months ago

transcriptomicsvisualizationrnaseqbayesianspatialsoftwaregeneexpressiondimensionreductionfeatureextractionsinglecellcpp

5.08 score 3 stars 9 scripts 105 downloads

alabaster.string - Save and Load Biostrings to/from File

Save Biostrings objects to file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 2 months ago

dataimportdatarepresentation

5.08 score 2 dependents 5 scripts 200 downloads

crisprVerse - Easily install and load the crisprVerse ecosystem for CRISPR gRNA design

The crisprVerse is a modular ecosystem of R packages developed for the design and manipulation of CRISPR guide RNAs (gRNAs). All packages share a common language and design principles. This package is designed to make it easy to install and load the crisprVerse packages in a single step. To learn more about the crisprVerse, visit <https://www.github.com/crisprVerse>.

Last updated 2 months ago

crisprfunctionalgenomicsgenetargetcrispr-analysiscrispr-designcrispr-targetgrnagrna-sequencegrna-sequences

5.08 score 12 stars 8 scripts 226 downloads

CNVMetrics - Copy Number Variant Metrics

The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.

Last updated 2 months ago

biologicalquestionsoftwarecopynumbervariationcnvcopy-number-variationmetricsr-language

5.08 score 4 stars 8 scripts 132 downloads

cTRAP - Identification of candidate causal perturbations from differential gene expression data

Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Last updated 2 months ago

differentialexpressiongeneexpressionrnaseqtranscriptomicspathwaysimmunooncologygenesetenrichmentbioconductorbioinformaticscmapgene-expressionl1000

5.08 score 5 stars 16 scripts 170 downloads

BiocSet - Representing Different Biological Sets

BiocSet displays different biological sets in a triple tibble format. These three tibbles are `element`, `set`, and `elementset`. The user has the abilty to activate one of these three tibbles to perform common functions from the dplyr package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.

Last updated 2 months ago

geneexpressiongokeggsoftware

5.06 score 4 dependents 32 scripts 656 downloads

PepSetTest - Peptide Set Test

Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.

Last updated 2 months ago

differentialexpressionregressionproteomicsmassspectrometry

5.04 score 2 stars 9 scripts 81 downloads

spqn - Spatial quantile normalization

The spqn package implements spatial quantile normalization (SpQN). This method was developed to remove a mean-correlation relationship in correlation matrices built from gene expression data. It can serve as pre-processing step prior to a co-expression analysis.

Last updated 2 months ago

networkinferencegraphandnetworknormalization

5.04 score 5 stars 22 scripts 134 downloads

CTexploreR - Explores Cancer Testis Genes

The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

Last updated 2 months ago

transcriptomicsepigeneticsdifferentialexpressiongeneexpressiondnamethylationexperimenthubsoftwaredataimportbioconductor

5.02 score 2 scripts 104 downloads

CelliD - Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data.

Last updated 2 months ago

rnaseqsinglecelldimensionreductionclusteringgenesetenrichmentgeneexpressionatacseqopenblascppopenmp

5.01 score 68 scripts 503 downloads

epiregulon.extra - Companion package to epiregulon with additional plotting, differential and graph functions

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Last updated 2 months ago

generegulationnetworkgeneexpressiontranscriptionchiponchipdifferentialexpressiongenetargetnormalizationgraphandnetwork

5.00 score 7 scripts 175 downloads

BioCartaImage - BioCarta Pathway Images

The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.

Last updated 2 months ago

softwarepathwaysbiocartavisualization

5.00 score 10 stars 6 scripts 116 downloads

TSAR - Thermal Shift Analysis in R

This package automates analysis workflow for Thermal Shift Analysis (TSA) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis.

Last updated 2 months ago

softwareshinyappsvisualizationqpcr

5.00 score 8 scripts 109 downloads

easylift - An R package to perform genomic liftover

The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor's GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.

Last updated 2 months ago

softwareworkflowstepsequencingcoveragegenomeassemblydataimport

5.00 score 5 stars 7 scripts 115 downloads

MAI - Mechanism-Aware Imputation

A two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present.

Last updated 2 months ago

softwaremetabolomicsstatisticalmethodclassificationimputation-methodsmachine-learningmissing-data

5.00 score 2 stars 6 scripts 153 downloads

shinyepico - ShinyÉPICo

ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.

Last updated 2 months ago

differentialmethylationdnamethylationmicroarraypreprocessingqualitycontrol

5.00 score 5 stars 1 scripts 177 downloads

EpiTxDb - Storing and accessing epitranscriptomic information using the AnnotationDbi interface

EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with.

Last updated 2 months ago

softwareepitranscriptomics

5.00 score 7 scripts 182 downloads

VariantExperiment - A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.

Last updated 2 months ago

infrastructuredatarepresentationsequencingannotationgenomeannotationgenotypingarray

5.00 score 1 stars 2 scripts 149 downloads

fmrs - Variable Selection in Finite Mixture of AFT Regression and FMR Models

The package obtains parameter estimation, i.e., maximum likelihood estimators (MLE), via the Expectation-Maximization (EM) algorithm for the Finite Mixture of Regression (FMR) models with Normal distribution, and MLE for the Finite Mixture of Accelerated Failure Time Regression (FMAFTR) subject to right censoring with Log-Normal and Weibull distributions via the EM algorithm and the Newton-Raphson algorithm (for Weibull distribution). More importantly, the package obtains the maximum penalized likelihood (MPLE) for both FMR and FMAFTR models (collectively called FMRs). A component-wise tuning parameter selection based on a component-wise BIC is implemented in the package. Furthermore, this package provides Ridge Regression and Elastic Net.

Last updated 2 months ago

survivalregressiondimensionreduction

5.00 score 3 stars 1 dependents 55 scripts 195 downloads

broadSeq - broadSeq : for streamlined exploration of RNA-seq data

This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

Last updated 2 months ago

geneexpressiondifferentialexpressionrnaseqtranscriptomicssequencingcoveragegenesetenrichmentgo

4.95 score 2 stars 5 scripts 122 downloads

iSEEfier - Streamlining the creation of initial states for starting an iSEE instance

iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).

Last updated 2 months ago

cellbasedassaysclusteringdimensionreductionfeatureextractionguigeneexpressionimmunooncologyshinyappssinglecellsoftwaretranscriptiontranscriptomicsvisualization

4.95 score 2 scripts 146 downloads

iSEEpathways - iSEE extension for panels related to pathway analysis

This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

Last updated 2 months ago

softwareinfrastructuredifferentialexpressiongeneexpressionguivisualizationpathwaysgenesetenrichmentgoshinyappsbioconductorhacktoberfestiseeiseeu

4.95 score 1 stars 10 scripts 120 downloads

alabaster.mae - Load and Save MultiAssayExperiments

Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 2 months ago

dataimportdatarepresentation

4.95 score 1 dependents 5 scripts 194 downloads

HPiP - Host-Pathogen Interaction Prediction

HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.

Last updated 2 months ago

proteomicssystemsbiologynetworkinferencestructuralpredictiongenepredictionnetwork

4.95 score 3 stars 6 scripts 130 downloads

HubPub - Utilities to create and use Bioconductor Hubs

HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket.

Last updated 2 months ago

dataimportinfrastructuresoftwarethirdpartyclientbioconductor-package

4.95 score 3 stars 4 scripts 240 downloads

InterCellar - InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell communication in one or multiple conditions.

Last updated 2 months ago

softwaresinglecellvisualizationgotranscriptomics

4.95 score 9 stars 7 scripts 180 downloads

ttgsea - Tokenizing Text of Gene Set Enrichment Analysis

Functional enrichment analysis methods such as gene set enrichment analysis (GSEA) have been widely used for analyzing gene expression data. GSEA is a powerful method to infer results of gene expression data at a level of gene sets by calculating enrichment scores for predefined sets of genes. GSEA depends on the availability and accuracy of gene sets. There are overlaps between terms of gene sets or categories because multiple terms may exist for a single biological process, and it can thus lead to redundancy within enriched terms. In other words, the sets of related terms are overlapping. Using deep learning, this pakage is aimed to predict enrichment scores for unique tokens or words from text in names of gene sets to resolve this overlapping set issue. Furthermore, we can coin a new term by combining tokens and find its enrichment score by predicting such a combined tokens.

Last updated 2 months ago

softwaregeneexpressiongenesetenrichment

4.95 score 3 dependents 3 scripts 156 downloads

aggregateBioVar - Differential Gene Expression Analysis for Multi-subject scRNA-seq

For single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates), this package contains tools to summarize single cell gene expression profiles at the level of subject. A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.

Last updated 2 months ago

softwaresinglecellrnaseqtranscriptomicstranscriptiongeneexpressiondifferentialexpression

4.95 score 5 stars 18 scripts 362 downloads

snifter - R wrapper for the python openTSNE library

Provides an R wrapper for the implementation of FI-tSNE from the python package openTNSE. See Poličar et al. (2019) <doi:10.1101/731877> and the algorithm described by Linderman et al. (2018) <doi:10.1038/s41592-018-0308-4>.

Last updated 2 months ago

dimensionreductionvisualizationsoftwaresinglecellsequencing

4.95 score 3 stars 3 scripts 311 downloads

padma - Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.

Last updated 2 months ago

softwarestatisticalmethodprincipalcomponentgeneexpressionpathwaysrnaseqbiocartamethylseq

4.95 score 3 stars 2 scripts 193 downloads

epigraHMM - Epigenomic R-based analysis with hidden Markov models

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

Last updated 2 months ago

chipseqatacseqdnaseseqhiddenmarkovmodelepigeneticszlibopenblascppopenmp

4.94 score 88 scripts 188 downloads

Pirat - Precursor or Peptide Imputation under Random Truncation

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

Last updated 2 months ago

proteomicsmassspectrometrypreprocessingsoftware

4.93 score 9 scripts 69 downloads

MBQN - Mean/Median-balanced quantile normalization

Modified quantile normalization for omics or other matrix-like data distorted in location and scale.

Last updated 2 months ago

normalizationpreprocessingproteomicssoftware

4.92 score 2 stars 14 scripts 154 downloads

plyxp - Data masks for SummarizedExperiment enabling dplyr-like manipulation

The package provides `rlang` data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for `plyxp` is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame.

Last updated 2 months ago

annotationgenomeannotationtranscriptomics

4.90 score 1 stars 3 scripts 46 downloads

HicAggR - Set of 3D genomic interaction analysis tools

This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values.

Last updated 2 months ago

softwarehicdataimportdatarepresentationnormalizationvisualizationdna3dstructureatacseqchipseqdnaseseqrnaseq

4.90 score 1 stars 3 scripts 140 downloads

scider - Spatial cell-type inter-correlation by density in R

scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

Last updated 2 months ago

spatialtranscriptomics

4.90 score 2 stars 3 scripts 113 downloads

scShapes - A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data

We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic.

Last updated 2 months ago

rnaseqsinglecellmultiplecomparisongeneexpression

4.90 score 8 stars 6 scripts 120 downloads

spiky - Spike-in calibration for cell-free MeDIP

spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.

Last updated 2 months ago

differentialmethylationdnamethylationnormalizationpreprocessingqualitycontrolsequencing

4.90 score 2 stars 3 scripts 140 downloads

immunotation - Tools for working with diverse immune genes

MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide. Reproducible and consistent annotation of HLA alleles in large-scale bioinformatics workflows remains challenging, because the available reference databases and software tools often use different HLA naming schemes. The package immunotation provides tools for consistent annotation of HLA genes in typical immunoinformatics workflows such as for example the prediction of MHC-presented peptides in different human donors. Converter functions that provide mappings between different HLA naming schemes are based on the MHC restriction ontology (MRO). The package also provides automated access to HLA alleles frequencies in worldwide human reference populations stored in the Allele Frequency Net Database.

Last updated 2 months ago

softwareimmunooncologybiomedicalinformaticsgeneticsannotation

4.90 score 8 stars 3 scripts 145 downloads

NewWave - Negative binomial model for scRNA-seq

A model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise.

Last updated 2 months ago

softwaregeneexpressiontranscriptomicssinglecellbatcheffectsequencingcoverageregressionbatch-effectsdimensionality-reductionnegative-binomialscrna-seq

4.90 score 4 stars 8 scripts 228 downloads

Melissa - Bayesian clustering and imputationa of single cell methylomes

Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking into account local correlations via a Generalised Linear Model approach and global similarities using a mixture modelling approach.

Last updated 2 months ago

immunooncologydnamethylationgeneexpressiongeneregulationepigeneticsgeneticsclusteringfeatureextractionregressionrnaseqbayesiankeggsequencingcoveragesinglecell

4.90 score 7 scripts 154 downloads

PanomiR - Detection of miRNAs that regulate interacting groups of pathways

PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

Last updated 2 months ago

geneexpressiongenesetenrichmentgenetargetmirnapathways

4.89 score 3 stars 13 scripts 154 downloads

RcwlPipelines - Bioinformatics pipelines based on Rcwl

A collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.

Last updated 2 months ago

softwareworkflowstepalignmentpreprocessingqualitycontroldnaseqrnaseqdataimportimmunooncology

4.89 score 1 dependents 26 scripts 233 downloads

mariner - Mariner: Explore the Hi-Cs

Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

Last updated 2 months ago

functionalgenomicsvisualizationhic

4.89 score 77 scripts 146 downloads

scatterHatch - Creates hatched patterns for scatterplots

The objective of this package is to efficiently create scatterplots where groups can be distinguished by color and texture. Visualizations in computational biology tend to have many groups making it difficult to distinguish between groups solely on color. Thus, this package is useful for increasing the accessibility of scatterplot visualizations to those with visual impairments such as color blindness.

Last updated 2 months ago

visualizationsinglecellcellbiologysoftwarespatial

4.89 score 7 stars 11 scripts 155 downloads

scanMiRApp - scanMiR shiny application

A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.

Last updated 2 months ago

mirnasequencematchingguishinyapps

4.88 score 19 scripts 162 downloads

MsDataHub - Mass Spectrometry Data on ExperimentHub

The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

Last updated 2 months ago

experimenthubsoftwaremassspectrometryproteomicsmetabolomicsbioconductordatamass-spectrometry

4.88 score 1 stars 1 scripts 133 downloads

ILoReg - ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

ILoReg is a tool for identification of cell populations from scRNA-seq data. In particular, ILoReg is useful for finding cell populations with subtle transcriptomic differences. The method utilizes a self-supervised learning method, called Iteratitive Clustering Projection (ICP), to find cluster probabilities, which are used in noise reduction prior to PCA and the subsequent hierarchical clustering and t-SNE steps. Additionally, functions for differential expression analysis to find gene markers for the populations and gene expression visualization are provided.

Last updated 2 months ago

singlecellsoftwareclusteringdimensionreductionrnaseqvisualizationtranscriptomicsdatarepresentationdifferentialexpressiontranscriptiongeneexpression

4.88 score 5 stars 2 scripts 130 downloads

AMARETTO - Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways.

Last updated 2 months ago

statisticalmethoddifferentialmethylationgeneregulationgeneexpressionmethylationarraytranscriptionpreprocessingbatcheffectdataimportmrnamicroarraymicrornaarrayregressionclusteringrnaseqcopynumbervariationsequencingmicroarraynormalizationnetworkbayesianexonarrayonechanneltwochannelproprietaryplatformsalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentmultiplecomparisonqualitycontroltimecourse

4.88 score 15 scripts 465 downloads

dStruct - Identifying differentially reactive regions from RNA structurome profiling data

dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al., Genome Biology, 2019 for the underlying method.

Last updated 2 months ago

statisticalmethodstructuralpredictionsequencingsoftware

4.86 score 2 stars 12 scripts 128 downloads

scDotPlot - Cluster a Single-cell RNA-seq Dot Plot

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

Last updated 2 months ago

softwarevisualizationdifferentialexpressiongeneexpressiontranscriptionrnaseqsinglecellsequencingclustering

4.85 score 2 stars 97 downloads

crisprShiny - Exploring curated CRISPR gRNAs via Shiny

Provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.

Last updated 2 months ago

crisprfunctionalgenomicsgenetargetguicrispr-analysiscrispr-designshiny

4.85 score 2 stars 8 scripts 126 downloads

tadar - Transcriptome Analysis of Differential Allelic Representation

This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.

Last updated 2 months ago

sequencingrnaseqsnpgenomicvariationvariantannotationdifferentialexpression

4.85 score 1 stars 4 scripts 150 downloads

CytoPipelineGUI - GUI's for visualization of flow cytometry data analysis pipelines

This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.

Last updated 2 months ago

flowcytometrypreprocessingqualitycontrolworkflowstepimmunooncologysoftwarevisualizationguishinyapps

4.85 score 2 scripts 110 downloads

multiWGCNA - multiWGCNA

An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.

Last updated 2 months ago

sequencingrnaseqgeneexpressiondifferentialexpressionregressionclustering

4.85 score 6 scripts 176 downloads

SVMDO - Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology

It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk and wilks lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets.

Last updated 2 months ago

genesetenrichmentdifferentialexpressionguiclassificationrnaseqtranscriptomicssurvivalmachine-learningrna-seqshiny

4.85 score 2 scripts 194 downloads

clevRvis - Visualization Techniques for Clonal Evolution

clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.

Last updated 2 months ago

softwareshinyappsvisualization

4.85 score 7 stars 2 scripts 145 downloads

AlphaBeta - Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze 'somatic' epimutations in the context of plant development and aging.

Last updated 2 months ago

epigeneticsfunctionalgenomicsgeneticsmathematicalbiology

4.85 score 8 scripts 252 downloads

ncGTW - Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.

Last updated 2 months ago

softwaremassspectrometrymetabolomicsalignment

4.85 score 7 stars 3 scripts 362 downloads

sSNAPPY - Single Sample directioNAl Pathway Perturbation analYsis

A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.

Last updated 2 months ago

softwaregeneexpressiongenesetenrichmentgenesignaling

4.83 score 1 stars 15 scripts 374 downloads

VplotR - Set of tools to make V-plots and compute footprint profiles

The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.

Last updated 2 months ago

nucleosomepositioningcoveragesequencingbiologicalquestionatacseqalignment

4.82 score 10 stars 11 scripts 174 downloads

evaluomeR - Evaluation of Bioinformatics Metrics

Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.

Last updated 2 months ago

clusteringclassificationfeatureextractionassessmentclustering-evaluationevaluomeevaluomermetrics

4.82 score 33 scripts 199 downloads

ADAPT - Analysis of Microbiome Differential Abundance by Pooling Tobit Models

ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones.

Last updated 2 months ago

differentialexpressionmicrobiomenormalizationsequencingmetagenomicssoftwaremultiplecomparisonopenblascpp

4.81 score 26 scripts

transmogR - Modify a set of reference sequences using a set of variants

transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.

Last updated 2 months ago

alignmentgenomicvariationsequencingtranscriptomevariant

4.81 score 2 scripts 133 downloads

spillR - Spillover Compensation in Mass Cytometry Data

Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

Last updated 2 months ago

flowcytometryimmunooncologymassspectrometrypreprocessingsinglecellsoftwarestatisticalmethodvisualizationregression

4.81 score 3 scripts 125 downloads

mina - Microbial community dIversity and Network Analysis

An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way.

Last updated 2 months ago

softwareworkflowstepcpp

4.81 score 5 stars 13 scripts 108 downloads

seahtrue - Seahtrue revives XF data for structured data analysis

Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.

Last updated 2 months ago

cellbasedassaysfunctionalpredictiondatarepresentationdataimportcellbiologycheminformaticsmetabolomicsmicrotitreplateassayvisualizationqualitycontrolbatcheffectexperimentaldesignpreprocessinggo

4.78 score 2 scripts 104 downloads

BiocBook - Write, containerize, publish and version Quarto books with Bioconductor

A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).

Last updated 2 months ago

infrastructurereportwritingsoftware

4.78 score 3 stars 4 scripts 125 downloads

alabaster.vcf - Save and Load Variant Data to/from File

Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 2 months ago

dataimportdatarepresentation

4.78 score 1 dependents 6 scripts 188 downloads

alabaster.bumpy - Save and Load BumpyMatrices to/from file

Save BumpyMatrix objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 2 months ago

dataimportdatarepresentation

4.78 score 1 dependents 5 scripts 156 downloads

biodbChebi - biodbChebi, a library for connecting to the ChEBI Database

The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields.

Last updated 2 months ago

softwareinfrastructuredataimport

4.78 score 2 stars 1 dependents 3 scripts 180 downloads

DeepPINCS - Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

The identification of novel compound-protein interaction (CPI) is important in drug discovery. Revealing unknown compound-protein interactions is useful to design a new drug for a target protein by screening candidate compounds. The accurate CPI prediction assists in effective drug discovery process. To identify potential CPI effectively, prediction methods based on machine learning and deep learning have been developed. Data for sequences are provided as discrete symbolic data. In the data, compounds are represented as SMILES (simplified molecular-input line-entry system) strings and proteins are sequences in which the characters are amino acids. The outcome is defined as a variable that indicates how strong two molecules interact with each other or whether there is an interaction between them. In this package, a deep-learning based model that takes only sequence information of both compounds and proteins as input and the outcome as output is used to predict CPI. The model is implemented by using compound and protein encoders with useful features. The CPI model also supports other modeling tasks, including protein-protein interaction (PPI), chemical-chemical interaction (CCI), or single compounds and proteins. Although the model is designed for proteins, DNA and RNA can be used if they are represented as sequences.

Last updated 2 months ago

softwarenetworkgraphandnetworkneuralnetworkopenjdk

4.78 score 2 dependents 4 scripts 153 downloads

supersigs - Supervised mutational signatures

Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).

Last updated 2 months ago

featureextractionclassificationregressionsequencingwholegenomesomaticmutation

4.78 score 3 stars 3 scripts 340 downloads

airpart - Differential cell-type-specific allelic imbalance

Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.

Last updated 2 months ago

singlecellrnaseqatacseqchipseqsequencinggeneregulationgeneexpressiontranscriptiontranscriptomevariantcellbiologyfunctionalgenomicsdifferentialexpressiongraphandnetworkregressionclusteringqualitycontrol

4.78 score 2 stars 2 scripts 316 downloads

nempi - Inferring unobserved perturbations from gene expression data

Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.

Last updated 2 months ago

softwaregeneexpressiondifferentialexpressiondifferentialmethylationgenesignalingpathwaysnetworkclassificationneuralnetworknetworkinferenceatacseqdnaseqrnaseqpooledscreenscrisprsinglecellsystemsbiology

4.78 score 2 stars 2 scripts 148 downloads

customCMPdb - Customize and Query Compound Annotation Database

This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.

Last updated 2 months ago

softwarecheminformaticsannotationhubsoftware

4.78 score 2 stars 4 scripts 184 downloads

sarks - Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Suffix Array Kernel Smoothing (see https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797), or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.

Last updated 2 months ago

motifdiscoverygeneregulationgeneexpressiontranscriptomicsrnaseqdifferentialexpressionfeatureextractionopenjdk

4.78 score 3 stars 3 scripts 163 downloads

VaSP - Quantification and Visualization of Variations of Splicing in Population

Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)

Last updated 2 months ago

rnaseqalternativesplicingdifferentialsplicingstatisticalmethodvisualizationpreprocessingclusteringdifferentialexpressionkeggimmunooncology3s-scoresalternative-splicingballgownrna-seqsplicingsqtlstatistics

4.78 score 3 stars 3 scripts 166 downloads

packFinder - de novo Annotation of Pack-TYPE Transposable Elements

Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).

Last updated 2 months ago

geneticssequencematchingannotationbioinformaticstext-mining

4.78 score 6 stars 6 scripts 190 downloads

MEB - A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data

This package provides a method to identify differential expression genes in the same or different species. Given that non-DE genes have some similarities in features, a scaling-free minimum enclosing ball (SFMEB) model is built to cover those non-DE genes in feature space, then those DE genes, which are enormously different from non-DE genes, being regarded as outliers and rejected outside the ball. The method on this package is described in the article 'A minimum enclosing ball method to detect differential expression genes for RNA-seq data'. The SFMEB method is extended to the scMEB method that considering two or more potential types of cells or unknown labels scRNA-seq dataset DEGs identification.

Last updated 2 months ago

differentialexpressiongeneexpressionnormalizationclassificationsequencing

4.78 score 1 scripts 140 downloads

NBAMSeq - Negative Binomial Additive Model for RNA-Seq Data

High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.

Last updated 2 months ago

rnaseqdifferentialexpressiongeneexpressionsequencingcoveragedifferential-expressiongene-expressiongeneralized-additive-modelsgeneralized-linear-modelsnegative-binomial-regressionsplines

4.78 score 2 stars 2 scripts 369 downloads

rmelting - R Interface to MELTING 5

R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.

Last updated 2 months ago

biomedicalinformaticscheminformaticsbioconductorbioinformaticsmelting-temperatureopenjdk

4.78 score 2 stars 10 scripts 139 downloads

decompTumor2Sig - Decomposition of individual tumors into mutational signatures by signature refitting

Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

Last updated 2 months ago

softwaresnpsequencingdnaseqgenomicvariationsomaticmutationbiomedicalinformaticsgeneticsbiologicalquestionstatisticalmethod

4.78 score 1 stars 1 dependents 10 scripts 355 downloads

ADAM - ADAM: Activity and Diversity Analysis Module

ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring togene diversity and activity. Each group of genes is called GFAG (Group of Functionally Associated Genes).

Last updated 2 months ago

genesetenrichmentpathwayskegggeneexpressionmicroarraycpp

4.78 score 1 dependents 8 scripts 458 downloads

ribosomeProfilingQC - Ribosome Profiling Quality Control

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

Last updated 2 months ago

riboseqsequencinggeneregulationqualitycontrolvisualizationcoverage

4.77 score 17 scripts 207 downloads

QTLExperiment - S4 classes for QTL summary statistics and metadata

QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the 'SummarizedExperiment' class and contains functions for creating, merging, and subsetting objects. 'QTLExperiment' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.

Last updated 2 months ago

functionalgenomicsdataimportdatarepresentationinfrastructuresequencingsnpsoftware

4.77 score 1 stars 1 dependents 13 scripts 116 downloads

eds - eds: Low-level reader for Alevin EDS format

This packages provides a single function, readEDS. This is a low-level utility for reading in Alevin EDS format into R. This function is not designed for end-users but instead the package is predominantly for simplifying package dependency graph for other Bioconductor packages.

Last updated 2 months ago

sequencingrnaseqgeneexpressionsinglecellcpp

4.76 score 1 dependents 19 scripts 654 downloads

MethReg - Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.

Last updated 2 months ago

methylationarrayregressiongeneexpressionepigeneticsgenetargettranscription

4.76 score 5 stars 19 scripts 171 downloads

plyinteractions - Extending tidy verbs to genomic interactions

Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.

Last updated 2 months ago

softwareinfrastructure

4.75 score 14 scripts 144 downloads

BioGA - Bioinformatics Genetic Algorithm (BioGA)

Genetic algorithm are a class of optimization algorithms inspired by the process of natural selection and genetics. This package allows users to analyze and optimize high throughput genomic data using genetic algorithms. The functions provided are implemented in C++ for improved speed and efficiency, with an easy-to-use interface for use within R.

Last updated 2 months ago

experimentaldesigntechnologycpp

4.74 score 5 scripts 120 downloads

smoothclust - smoothclust

Method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses.

Last updated 2 months ago

spatialsinglecelltranscriptomicsgeneexpressionclustering

4.74 score 1 stars 7 scripts 173 downloads

CBEA - Competitive Balances for Taxonomic Enrichment Analysis in R

This package implements CBEA, a method to perform set-based analysis for microbiome relative abundance data. This approach constructs a competitive balance between taxa within the set and remainder taxa per sample. More details can be found in the Nguyen et al. 2021+ manuscript. Additionally, this package adds support functions to help users perform taxa-set enrichment analyses using existing gene set analysis methods. In the future we hope to also provide curated knowledge driven taxa sets.

Last updated 2 months ago

softwaremicrobiomemetagenomicsgenesetenrichmentdataimportenrichment-analysistaxonomic-enrichment-analysiscpp

4.74 score 5 stars 11 scripts 206 downloads

MatrixQCvis - Shiny-based interactive data-quality exploration for omics data

Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualizations include amongst others bar- and violin plots of the (count/intensity) values, mean vs standard deviation plots, MA plots, empirical cumulative distribution function (ECDF) plots, visualizations of the distances between samples, and multiple types of dimension reduction plots. Furthermore, MatrixQCvis allows for differential expression analysis based on the limma (moderated t-tests) and proDA (Wald tests) packages. MatrixQCvis builds upon the popular Bioconductor SummarizedExperiment S4 class and enables thus the facile integration into existing workflows. The package is especially tailored towards metabolomics and proteomics mass spectrometry data, but also allows to assess the data quality of other data types that can be represented in a SummarizedExperiment object.

Last updated 2 months ago

visualizationshinyappsguiqualitycontroldimensionreductionmetabolomicsproteomicstranscriptomics

4.74 score 4 scripts 374 downloads

survClust - Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning

survClust is an outcome weighted integrative clustering algorithm used to classify multi-omic samples on their available time to event information. The resulting clusters are cross-validated to avoid over overfitting and output classification of samples that are molecularly distinct and clinically meaningful. It takes in binary (mutation) as well as continuous data (other omic types).

Last updated 2 months ago

softwareclusteringsurvivalclassificationcpp

4.74 score 16 stars 17 scripts 83 downloads

decontX - Decontamination of single cell genomics data

This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

Last updated 2 months ago

singlecellbayesiancpp

4.73 score 27 scripts 440 downloads

MesKit - A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to depict mutational profiles, measure heterogeneity within or between tumors from the same patient, track evolutionary dynamics, as well as characterize mutational patterns on different levels. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the interpretation of tumor heterogeneity and the understanding of evolutionary relationship between regions in MRS study.

Last updated 2 months ago

4.73 score 1 dependents 18 scripts 168 downloads

PhosR - A set of methods and tools for comprehensive analysis of phosphoproteomics data

PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.

Last updated 2 months ago

softwareresearchfieldproteomics

4.71 score 51 scripts 224 downloads

tidysbml - Extract SBML's data into dataframes

Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the 'notes' subelement and one set of columns for the content of the 'annotation' subelement.

Last updated 2 months ago

graphandnetworknetworkpathwayssoftware

4.70 score 2 scripts

tpSVG - Thin plate models to detect spatially variable genes

The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis.

Last updated 2 months ago

spatialtranscriptomicsgeneexpressionsoftwarestatisticalmethoddimensionreductionregressionpreprocessingspatially-resolvespatially-variable-genes

4.70 score 2 stars 2 scripts 129 downloads

fenr - Fast functional enrichment for interactive applications

Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, Bioplanet and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.

Last updated 2 months ago

functionalpredictiondifferentialexpressiongenesetenrichmentgokeggreactomeproteomics

4.70 score 3 scripts 144 downloads

HGC - A fast hierarchical graph-based clustering method

HGC (short for Hierarchical Graph-based Clustering) is an R package for conducting hierarchical clustering on large-scale single-cell RNA-seq (scRNA-seq) data. The key idea is to construct a dendrogram of cells on their shared nearest neighbor (SNN) graph. HGC provides functions for building graphs and for conducting hierarchical clustering on the graph. The users with old R version could visit https://github.com/XuegongLab/HGC/tree/HGC4oldRVersion to get HGC package built for R 3.6.

Last updated 2 months ago

singlecellsoftwareclusteringrnaseqgraphandnetworkdnaseqcpp

4.70 score 25 scripts 158 downloads

epidecodeR - epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

epidecodeR is a package capable of analysing impact of degree of DNA/RNA epigenetic chemical modifications on dysregulation of genes or proteins. This package integrates chemical modification data generated from a host of epigenomic or epitranscriptomic techniques such as ChIP-seq, ATAC-seq, m6A-seq, etc. and dysregulated gene lists in the form of differential gene expression, ribosome occupancy or differential protein translation and identify impact of dysregulation of genes caused due to varying degrees of chemical modifications associated with the genes. epidecodeR generates cumulative distribution function (CDF) plots showing shifts in trend of overall log2FC between genes divided into groups based on the degree of modification associated with the genes. The tool also tests for significance of difference in log2FC between groups of genes.

Last updated 2 months ago

differentialexpressiongeneregulationhistonemodificationfunctionalpredictiontranscriptiongeneexpressionepitranscriptomicsepigeneticsfunctionalgenomicssystemsbiologytranscriptomicschiponchipdifferential-expressiongenomicsgenomics-visualization

4.70 score 5 stars 1 scripts 140 downloads

barcodetrackR - Functions for Analyzing Cellular Barcoding Data

barcodetrackR is an R package developed for the analysis and visualization of clonal tracking data. Data required is samples and tag abundances in matrix form. Usually from cellular barcoding experiments, integration site retrieval analyses, or similar technologies.

Last updated 2 months ago

softwarevisualizationsequencing

4.70 score 5 stars 6 scripts 253 downloads

midasHLA - R package for immunogenomics data handling and association analysis

MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.

Last updated 2 months ago

cellbiologygeneticsstatisticalmethod

4.70 score 3 scripts 182 downloads

wpm - Well Plate Maker

The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects. In particular, it helps controlling the "plate effect" thanks to its ability to randomize samples over multiple well plates. The algorithm for placing the samples is inspired by the backtracking algorithm: the samples are placed at random while respecting specific spatial constraints.

Last updated 2 months ago

guiproteomicsmassspectrometrybatcheffectexperimentaldesign

4.70 score 5 stars 7 scripts 164 downloads

weitrix - Tools for matrices with precision weights, test and explore weighted or sparse data

Data type and tools for working with matrices having precision weights and missing data. This package provides a common representation and tools that can be used with many types of high-throughput data. The meaning of the weights is compatible with usage in the base R function "lm" and the package "limma". Calibrate weights to account for known predictors of precision. Find rows with excess variability. Perform differential testing and find rows with the largest confident differences. Find PCA-like components of variation even with many missing values, rotated so that individual components may be meaningfully interpreted. DelayedArray matrices and BiocParallel are supported.

Last updated 2 months ago

softwaredatarepresentationdimensionreductiongeneexpressiontranscriptomicsrnaseqsinglecellregression

4.70 score 8 scripts 160 downloads

TOP - TOP Constructs Transferable Model Across Gene Expression Platforms

TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.

Last updated 2 months ago

softwaresurvivalgeneexpression

4.69 score 49 scripts 112 downloads

DelayedTensor - R package for sparse and out-of-core arithmetic and decomposition of Tensor

DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum.

Last updated 2 months ago

softwareinfrastructuredatarepresentationdimensionreduction

4.68 score 4 stars 3 scripts 138 downloads

immunogenViewer - Visualization and evaluation of protein immunogens

Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins.

Last updated 2 months ago

featureextractionproteomicssoftwarevisualization

4.65 score 9 scripts 105 downloads

DeepTarget - Deep characterization of cancer drugs

This package predicts a drug’s primary target(s) or secondary target(s) by integrating large-scale genetic and drug screens from the Cancer Dependency Map project run by the Broad Institute. It further investigates whether the drug specifically targets the wild-type or mutated target forms. To show how to use this package in practice, we provided sample data along with step-by-step example.

Last updated 2 months ago

genetargetgenepredictionpathwaysgeneexpressionrnaseqimmunooncologydifferentialexpressiongenesetenrichmentreportwritingcrispr

4.65 score 1 scripts 121 downloads

multistateQTL - Toolkit for the analysis of multi-state QTL data

A collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package 'multistateQTL' contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a 'QTLExperiment' object, which is based on the 'SummarisedExperiment' framework.

Last updated 2 months ago

functionalgenomicsgeneexpressionsequencingvisualizationsnpsoftware

4.65 score 9 scripts 128 downloads

DELocal - Identifies differentially expressed genes with respect to other local genes

The goal of DELocal is to identify DE genes compared to their neighboring genes from the same chromosomal location. It has been shown that genes of related functions are generally very far from each other in the chromosome. DELocal utilzes this information to identify DE genes comparing with their neighbouring genes.

Last updated 2 months ago

geneexpressiondifferentialexpressionrnaseqtranscriptomics

4.65 score 1 dependents 3 scripts 145 downloads

EpiMix - EpiMix: an integrative tool for the population-level analysis of DNA methylation

EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.

Last updated 2 months ago

softwareepigeneticspreprocessingdnamethylationgeneexpressiondifferentialmethylation

4.65 score 1 stars 1 dependents 7 scripts 140 downloads

fgga - Hierarchical ensemble method based on factor graph

Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models.

Last updated 2 months ago

softwarestatisticalmethodclassificationnetworknetworkinferencesupportvectormachinegraphandnetworkgo

4.65 score 3 stars 6 scripts 141 downloads

Informeasure - R implementation of information measures

This package consolidates a comprehensive set of information measurements, encompassing mutual information, conditional mutual information, interaction information, partial information decomposition, and part mutual information.

Last updated 2 months ago

geneexpressionnetworkinferencenetworksoftware

4.65 score 3 stars 4 scripts 116 downloads

hca - Exploring the Human Cell Atlas Data Coordinating Platform

This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes; corresponding `*_details()` are available for individual entries of each index. File-based resources can be downloaded using `files_download()`. Advanced use of the package allows the user to page through large result sets, and to flexibly query the 'list-of-lists' structure representing query responses.

Last updated 2 months ago

softwaresinglecell

4.64 score 55 scripts 139 downloads

alabaster.files - Wrappers to Save Common File Formats

Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

Last updated 2 months ago

datarepresentationdataimport

4.62 score 21 scripts 104 downloads

Cepo - Cepo for the identification of differentially stable genes

Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.

Last updated 2 months ago

classificationgeneexpressionsinglecellsoftwaresequencingdifferentialexpression

4.62 score 1 dependents 14 scripts 262 downloads

corral - Correspondence Analysis for Single Cell Data

Correspondence analysis (CA) is a matrix factorization method, and is similar to principal components analysis (PCA). Whereas PCA is designed for application to continuous, approximately normally distributed data, CA is appropriate for non-negative, count-based data that are in the same additive scale. The corral package implements CA for dimensionality reduction of a single matrix of single-cell data, as well as a multi-table adaptation of CA that leverages data-optimized scaling to align data generated from different sequencing platforms by projecting into a shared latent space. corral utilizes sparse matrices and a fast implementation of SVD, and can be called directly on Bioconductor objects (e.g., SingleCellExperiment) for easy pipeline integration. The package also includes additional options, including variations of CA to address overdispersion in count data (e.g., Freeman-Tukey chi-squared residual), as well as the option to apply CA-style processing to continuous data (e.g., proteomic TOF intensities) with the Hellinger distance adaptation of CA.

Last updated 2 months ago

batcheffectdimensionreductiongeneexpressionpreprocessingprincipalcomponentsequencingsinglecellsoftwarevisualization

4.62 score 21 scripts 182 downloads

Dune - Improving replicability in single-cell RNA-Seq cell type discovery

Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.

Last updated 2 months ago

clusteringgeneexpressionrnaseqsoftwaresinglecelltranscriptomicsvisualization

4.61 score 41 scripts 140 downloads

DNABarcodes - A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments

The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.

Last updated 2 months ago

preprocessingsequencingcppopenmp

4.61 score 27 scripts 406 downloads

zitools - Analysis of zero-inflated count data

zitools allows for zero inflated count data analysis by either using down-weighting of excess zeros or by replacing an appropriate proportion of excess zeros with NA. Through overloading frequently used statistical functions (such as mean, median, standard deviation), plotting functions (such as boxplots or heatmap) or differential abundance tests, it allows a wide range of downstream analyses for zero-inflated data in a less biased manner. This becomes applicable in the context of microbiome analyses, where the data is often overdispersed and zero-inflated, therefore making data analysis extremly challenging.

Last updated 2 months ago

softwarestatisticalmethodmicrobiome

4.60 score 6 scripts 90 downloads

GNOSIS - Genomics explorer using statistical and survival analysis in R

GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.

Last updated 2 months ago

softwareshinyappssurvivalgui

4.60 score 4 stars 2 scripts 148 downloads

magpie - MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation

This package aims to perform power analysis for the MeRIP-seq study. It calculates FDR, FDC, power, and precision under various study design parameters, including but not limited to sample size, sequencing depth, and testing method. It can also output results into .xlsx files or produce corresponding figures of choice.

Last updated 2 months ago

epitranscriptomicsdifferentialmethylationsequencingrnaseqsoftware

4.60 score 40 scripts 119 downloads

stJoincount - stJoincount - Join count statistic for quantifying spatial correlation between clusters

stJoincount facilitates the application of join count analysis to spatial transcriptomic data generated from the 10x Genomics Visium platform. This tool first converts a labeled spatial tissue map into a raster object, in which each spatial feature is represented by a pixel coded by label assignment. This process includes automatic calculation of optimal raster resolution and extent for the sample. A neighbors list is then created from the rasterized sample, in which adjacent and diagonal neighbors for each pixel are identified. After adding binary spatial weights to the neighbors list, a multi-categorical join count analysis is performed to tabulate "joins" between all possible combinations of label pairs. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance.

Last updated 2 months ago

transcriptomicsclusteringspatialbiocviewssoftware

4.60 score 4 stars 3 scripts 170 downloads

RESOLVE - RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes

Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization), a framework that allows the efficient extraction and assignment of mutational signatures. RESOLVE implements a novel algorithm that enables (i) the efficient extraction, (ii) exposure estimation, and (iii) confidence assessment during the computational inference of mutational signatures.

Last updated 2 months ago

biomedicalinformaticssomaticmutation

4.60 score 1 stars 3 scripts 147 downloads

oncoscanR - Secondary analyses of CNV data (HRD and more)

The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.

Last updated 2 months ago

copynumbervariationmicroarraysoftware

4.60 score 2 stars 6 scripts 152 downloads

rifi - 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.

Last updated 2 months ago

rnaseqdifferentialexpressiongeneregulationtranscriptomicsregressionmicroarraysoftware

4.60 score 1 scripts 144 downloads

RAREsim - Simulation of Rare Variant Genetic Data

Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

Last updated 2 months ago

geneticssoftwarevariantannotationsequencing

4.60 score 4 stars 4 scripts 108 downloads

terraTCGAdata - OpenAccess TCGA Data on Terra as MultiAssayExperiment

Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.

Last updated 2 months ago

softwareinfrastructuredataimportbioconductor-package

4.60 score 4 scripts 187 downloads

MBECS - Evaluation and correction of batch effects in microbiome data-sets

The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

Last updated 2 months ago

batcheffectmicrobiomereportwritingvisualizationnormalizationqualitycontrol

4.60 score 4 stars 4 scripts 284 downloads

OGRE - Calculate, visualize and analyse overlap between genomic regions

OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.

Last updated 2 months ago

softwareworkflowstepbiologicalquestionannotationmetagenomicsvisualizationsequencing

4.60 score 2 stars 4 scripts 154 downloads

TargetDecoy - Diagnostic Plots to Evaluate the Target Decoy Approach

A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum is then assigned to the theoretical peptide with the best score, which is also referred to as the peptide to spectrum match (PSM). It is of course crucial for the downstream analysis to evaluate the quality of these matches. Therefore False Discovery Rate (FDR) control is used to return a reliable list PSMs. The FDR, however, requires a good characterisation of the score distribution of PSMs that are matched to the wrong peptide (bad target hits). In proteomics, the target decoy approach (TDA) is typically used for this purpose. The TDA method matches the spectra to a database of real (targets) and nonsense peptides (decoys). A popular approach to generate these decoys is to reverse the target database. Hence, all the PSMs that match to a decoy are known to be bad hits and the distribution of their scores are used to estimate the distribution of the bad scoring target PSMs. A crucial assumption of the TDA is that the decoy PSM hits have similar properties as bad target hits so that the decoy PSM scores are a good simulation of the target PSM scores. Users, however, typically do not evaluate these assumptions. To this end we developed TargetDecoy to generate diagnostic plots to evaluate the quality of the target decoy method.

Last updated 2 months ago

massspectrometryproteomicsqualitycontrolsoftwarevisualizationbioconductormass-spectrometry

4.60 score 1 stars 9 scripts 190 downloads

IntramiRExploreR - Predicting Targets for Drosophila Intragenic miRNAs

Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.

Last updated 2 months ago

softwaremicroarraygenetargetstatisticalmethodgeneexpressiongeneprediction

4.60 score 4 scripts 182 downloads

svaRetro - Retrotransposed transcript detection from structural variants

svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.

Last updated 2 months ago

dataimportsequencingannotationgeneticsvariantannotationcoveragevariantdetection

4.60 score 4 scripts 156 downloads

iPath - iPath pipeline for detecting perturbed pathways at individual level

iPath is the Bioconductor package used for calculating personalized pathway score and test the association with survival outcomes. Abundant single-gene biomarkers have been identified and used in the clinics. However, hundreds of oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. We believe individual-level expression patterns of pre-defined pathways or gene sets are better biomarkers than single genes. In this study, we devised a computational method named iPath to identify prognostic biomarker pathways, one sample at a time. To test its utility, we conducted a pan-cancer analysis across 14 cancer types from The Cancer Genome Atlas and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor stage classifications. We found that pathway-based biomarkers are more robust and effective than single genes.

Last updated 2 months ago

pathwayssoftwaregeneexpressionsurvivalcpp

4.60 score 2 stars 3 scripts 116 downloads

segmenter - Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.

Last updated 2 months ago

softwarehistonemodificationbioconductorchromhmmsegmentation-an

4.60 score 4 stars 9 scripts 212 downloads

RCSL - Rank Constrained Similarity Learning for single cell RNA sequencing data

A novel clustering algorithm and toolkit RCSL (Rank Constrained Similarity Learning) to accurately identify various cell types using scRNA-seq data from a complex tissue. RCSL considers both lo-cal similarity and global similarity among the cells to discern the subtle differences among cells of the same type as well as larger differences among cells of different types. RCSL uses Spearman’s rank correlations of a cell’s expression vector with those of other cells to measure its global similar-ity, and adaptively learns neighbour representation of a cell as its local similarity. The overall similar-ity of a cell to other cells is a linear combination of its global similarity and local similarity.

Last updated 2 months ago

singlecellsoftwareclusteringdimensionreductionrnaseqvisualizationsequencing

4.60 score 2 stars 10 scripts 164 downloads

KBoost - Inference of gene regulatory networks from gene expression data

Reconstructing gene regulatory networks and transcription factor activity is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-art algorithm are often not able to handle large amounts of data. Furthermore, many of the present methods predict numerous false positives and are unable to integrate other sources of information such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. KBoost can also use a prior network built on previously known transcription factor targets. We have benchmarked KBoost using three different datasets against other high performing algorithms. The results show that our method compares favourably to other methods across datasets.

Last updated 2 months ago

networkgraphandnetworkbayesiannetworkinferencegeneregulationtranscriptomicssystemsbiologytranscriptiongeneexpressionregressionprincipalcomponent

4.60 score 4 stars 9 scripts 106 downloads

cellmigRation - Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.

Last updated 2 months ago

cellbiologydatarepresentationdataimportbioconductor-packagecell-trackingshinytrajectory-analysis

4.60 score 4 scripts 130 downloads

sitadela - An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.

Last updated 2 months ago

softwareworkflowsteprnaseqtranscriptionsequencingtranscriptomicsbiomedicalinformaticsfunctionalgenomicssystemsbiologyalternativesplicingdataimportchipseq

4.60 score 2 scripts 122 downloads

TrajectoryGeometry - This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.

Last updated 2 months ago

biologicalquestionstatisticalmethodgeneexpressionsinglecell

4.60 score 7 scripts 114 downloads

CAEN - Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

With the development of high-throughput techniques, more and more gene expression analysis tend to replace hybridization-based microarrays with the revolutionary technology.The novel method encodes the category again by employing the rank of samples for each gene in each class. We then consider the correlation coefficient of gene and class with rank of sample and new rank of category. The highest correlation coefficient genes are considered as the feature genes which are most effective to classify the samples.

Last updated 2 months ago

differentialexpressionsequencingclassificationrnaseqatacseqsinglecellgeneexpressionripseq

4.60 score 2 scripts 119 downloads

GEOfastq - Downloads ENA Fastqs With GEO Accessions

GEOfastq is used to download fastq files from the European Nucleotide Archive (ENA) starting with an accession from the Gene Expression Omnibus (GEO). To do this, sample metadata is retrieved from GEO and the Sequence Read Archive (SRA). SRA run accessions are then used to construct FTP and aspera download links for fastq files generated by the ENA.

Last updated 2 months ago

rnaseqdataimportbioinformaticsfastqgene-expressiongeorna-seq

4.60 score 4 stars 6 scripts 218 downloads

bnem - Training of logical models from indirect measurements of perturbation experiments

bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).

Last updated 2 months ago

pathwayssystemsbiologynetworkinferencenetworkgeneexpressiongeneregulationpreprocessing

4.60 score 2 stars 5 scripts 166 downloads

marr - Maximum rank reproducibility

marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample pairs per feature in high-dimensional biological replicate experiments. The user-friendly plot functions in this package also plot histograms of the reproducibility of features per sample pair and sample pairs per feature. Furthermore, our approach also allows the users to select optimal filtering threshold values for the identification of reproducible features and sample pairs based on output visualization checks (histograms). This package also provides the subset of data filtered by reproducible features and/or sample pairs.

Last updated 2 months ago

qualitycontrolmetabolomicsmassspectrometryrnaseqchipseqcpp

4.60 score 2 stars 4 scripts 172 downloads

metabolomicsWorkbenchR - Metabolomics Workbench in R

This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included.

Last updated 2 months ago

softwaremetabolomics

4.60 score 8 scripts 204 downloads

NoRCE - NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint to a functional association. We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast.

Last updated 2 months ago

biologicalquestiondifferentialexpressiongenomeannotationgenesetenrichmentgenetargetgenomeassemblygo

4.60 score 1 stars 6 scripts 158 downloads

reconsi - Resampling Collapsed Null Distributions for Simultaneous Inference

Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts.

Last updated 2 months ago

metagenomicsmicrobiomemultiplecomparisonflowcytometry

4.60 score 2 stars 2 scripts 130 downloads

easyreporting - Helps creating report for improving Reproducible Computational Research

An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software even without knowing rmarkdown language. Best if implemented in functions as "recursive" style programming.

Last updated 2 months ago

reportwriting

4.60 score 2 stars 2 scripts 160 downloads

brendaDb - The BRENDA Enzyme Database

R interface for importing and analyzing enzyme information from the BRENDA database.

Last updated 2 months ago

thirdpartyclientannotationdataimportbrendadatabaseenzymehacktoberfest

4.60 score 2 stars 4 scripts 153 downloads

AWFisher - An R package for fast computing for adaptively weighted fisher's method

Implementation of the adaptively weighted fisher's method, including fast p-value computing, variability index, and meta-pattern.

Last updated 2 months ago

statisticalmethodsoftware

4.60 score 4 stars 4 scripts 298 downloads

GNET2 - Constructing gene regulatory networks from expression data through functional module inference

Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.

Last updated 2 months ago

geneexpressionregressionnetworknetworkinferencesoftwarecpp

4.60 score 2 stars 3 scripts 138 downloads

SMAD - Statistical Modelling of AP-MS Data (SMAD)

Assigning probability scores to protein interactions captured in affinity purification mass spectrometry (AP-MS) expriments to infer protein-protein interactions. The output would facilitate non-specific background removal as contaminants are commonly found in AP-MS data.

Last updated 2 months ago

massspectrometryproteomicssoftwarecpp

4.60 score 3 scripts 161 downloads

pmp - Peak Matrix Processing and signal batch correction for metabolomics datasets

Methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.

Last updated 2 months ago

massspectrometrymetabolomicssoftwarequalitycontrolbatcheffect

4.60 score 33 scripts 229 downloads

dce - Pathway Enrichment Based on Differential Causal Effects

Compute differential causal effects (dce) on (biological) networks. Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression. If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero. We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.

Last updated 5 days ago

softwarestatisticalmethodgraphandnetworkregressiongeneexpressiondifferentialexpressionnetworkenrichmentnetworkkeggbioconductorcausality

4.59 score 13 stars 4 scripts 183 downloads

NetActivity - Compute gene set scores from a deep learning framework

#' NetActivity enables to compute gene set scores from previously trained sparsely-connected autoencoders. The package contains a function to prepare the data (`prepareSummarizedExperiment`) and a function to compute the gene set scores (`computeGeneSetScores`). The package `NetActivityData` contains different pre-trained models to be directly applied to the data. Alternatively, the users might use the package to compute gene set scores using custom models.

Last updated 2 months ago

rnaseqmicroarraytranscriptionfunctionalgenomicsgogeneexpressionpathwayssoftware

4.59 score 26 scripts 138 downloads

ClusterFoldSimilarity - Calculate similarity of clusters from different single cell samples using foldchanges

This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m

Last updated 2 months ago

singlecellclusteringfeatureextractiongraphandnetworkgenetargetrnaseq

4.59 score 11 scripts 106 downloads

goSorensen - Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.

Last updated 2 months ago

annotationgogenesetenrichmentsoftwaremicroarraypathwaysgeneexpressionmultiplecomparisongraphandnetworkreactomeclusteringkegg

4.56 score 12 scripts 177 downloads

MAPFX - MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.

Last updated 2 months ago

softwareflowcytometrycellbasedassayssinglecellproteomicsclustering

4.54 score 1 stars 157 downloads

UPDhmm - Detecting Uniparental Disomy through NGS trio data

Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent, rather than one copy from each parent. This package contains a HMM for detecting UPDs through HTS (High Throughput Sequencing) data from trio assays. By analyzing the genotypes in the trio, the model infers a hidden state (normal, father isodisomy, mother isodisomy, father heterodisomy and mother heterodisomy).

Last updated 2 months ago

softwarehiddenmarkovmodelgenetics

4.54 score 1 stars 3 scripts 137 downloads

simPIC - simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data

simPIC is a package for simulating single-cell ATAC-seq count data. It provides a user-friendly, well documented interface for data simulation. Functions are provided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets.

Last updated 2 months ago

singlecellatacseqsoftwaresequencingimmunooncologydataimport

4.54 score 3 scripts 120 downloads

DCATS - Differential Composition Analysis Transformed by a Similarity matrix

Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.

Last updated 2 months ago

singlecellnormalization

4.53 score 34 scripts 152 downloads

FuseSOM - A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (`FuseSOM`) is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by combining a `Self Organizing Map` architecture and a `Multiview` integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays.

Last updated 2 months ago

singlecellcellbasedassaysclusteringspatial

4.53 score 1 stars 17 scripts 136 downloads

RedisParam - Provide a 'redis' back-end for BiocParallel

This package provides a Redis-based back-end for BiocParallel, enabling an alternative mechanism for distributed computation. The The 'manager' distributes tasks to a 'worker' pool through a central Redis server, rather than directly to workers as with other BiocParallel implementations. This means that the worker pool can change dynamically during job evaluation. All features of BiocParallel are supported, including reproducible random number streams, logging to the manager, and alternative 'load balancing' task distributions.

Last updated 2 months ago

infrastructure

4.53 score 17 scripts 128 downloads

Macarron - Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

Macarron is a workflow for the prioritization of potentially bioactive metabolites from metabolomics experiments. Prioritization integrates strengths of evidences of bioactivity such as covariation with a known metabolite, abundance relative to a known metabolite and association with an environmental or phenotypic indicator of bioactivity. Broadly, the workflow consists of stratified clustering of metabolic spectral features which co-vary in abundance in a condition, transfer of functional annotations, estimation of relative abundance and differential abundance analysis to identify associations between features and phenotype/condition.

Last updated 2 months ago

sequencingmetabolomicscoveragefunctionalpredictionclustering

4.51 score 13 scripts 200 downloads

mumosa - Multi-Modal Single-Cell Analysis Methods

Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities.

Last updated 2 months ago

immunooncologysinglecellrnaseq

4.51 score 13 scripts 154 downloads

ribor - An R Interface for Ribo Files

The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.

Last updated 2 months ago

softwareinfrastructure

4.51 score 32 scripts 142 downloads

SQLDataFrame - Representation of SQL tables in DataFrame metaphor

Implements bindings for SQL tables that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows SQL-derived data to be easily used inside other Bioconductor objects (e.g., SummarizedExperiments) while keeping everything on disk.

Last updated 2 months ago

datarepresentationinfrastructuresoftware

4.51 score 2 stars 5 scripts 130 downloads

comapr - Crossover analysis and genetic map construction

comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals. Visualisation functions for plotting interval-based genetic map or cumulative genetic distances are implemented, which help reveal the variation of crossovers landscapes across the genome and across individuals.

Last updated 3 hours ago

softwaresinglecellvisualizationgenetics

4.48 score 4 scripts 174 downloads

BEARscc - BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)

BEARscc is a noise estimation and injection tool that is designed to assess putative single-cell RNA-seq clusters in the context of experimental noise estimated by ERCC spike-in controls.

Last updated 5 days ago

immunooncologysinglecellclusteringtranscriptomics

4.48 score 1 scripts 172 downloads

ramr - Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

ramr is an R package for detection of epimutations (i.e., infrequent aberrant DNA methylation events) in large data sets obtained by methylation profiling using array or high-throughput methylation sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.

Last updated 5 days ago

dnamethylationdifferentialmethylationepigeneticsmethylationarraymethylseqaberrant-methylationbioconductordna-methylationepimutationmethylation-microarraysnext-generation-sequencing

4.48 score 5 scripts 137 downloads

scoup - Simulate Codons with Darwinian Selection Modelled as an OU Process

An elaborate molecular evolutionary framework that facilitates straightforward simulation of codon genetic sequences subjected to different degrees and/or patterns of Darwinian selection. The model was built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enabled realistic evolutionary process of living organisms to be reproduced seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated herein. Consequently, otherwise complex biological processes, such as the effect of the interplay between genetic drift and mutation on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and deterministic fitness landscape update techniques are also available.

Last updated 5 days ago

alignmentclassificationcomparativegenomicsdataimportgeneticsmathematicalbiologyresearchfieldsequencingsequencematchingsoftwarestatisticalmethodworkflowstep

4.48 score 8 scripts 54 downloads

xenLite - Simple classes and methods for managing Xenium datasets

Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

Last updated 2 months ago

infrastructure

4.48 score 1 stars 4 scripts

hdxmsqc - An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments

The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.

Last updated 2 months ago

qualitycontroldataimportproteomicsmassspectrometrymetabolomics

4.48 score 2 scripts 159 downloads

dinoR - Differential NOMe-seq analysis

dinoR tests for significant differences in NOMe-seq footprints between two conditions, using genomic regions of interest (ROI) centered around a landmark, for example a transcription factor (TF) motif. This package takes NOMe-seq data (GCH methylation/protection) in the form of a Ranged Summarized Experiment as input. dinoR can be used to group sequencing fragments into 3 or 5 categories representing characteristic footprints (TF bound, nculeosome bound, open chromatin), plot the percentage of fragments in each category in a heatmap, or averaged across different ROI groups, for example, containing a common TF motif. It is designed to compare footprints between two sample groups, using edgeR's quasi-likelihood methods on the total fragment counts per ROI, sample, and footprint category.

Last updated 2 months ago

nucleosomepositioningepigeneticsmethylseqdifferentialmethylationcoveragetranscriptionsequencingsoftware

4.48 score 7 scripts 122 downloads

MIRit - Integrate microRNA and gene expression to decipher pathway complexity

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

Last updated 2 months ago

softwaregeneregulationnetworkenrichmentnetworkinferenceepigeneticsfunctionalgenomicssystemsbiologynetworkpathwaysgeneexpressiondifferentialexpressionmirnamirna-mrna-interactionmirna-seqmirnaseq-analysiscpp

4.48 score 2 scripts 140 downloads

RNAseqCovarImpute - Impute Covariate Data in RNA Sequencing Studies

The RNAseqCovarImpute package makes linear model analysis for RNA sequencing read counts compatible with multiple imputation (MI) of missing covariates. A major problem with implementing MI in RNA sequencing studies is that the outcome data must be included in the imputation prediction models to avoid bias. This is difficult in omics studies with high-dimensional data. The first method we developed in the RNAseqCovarImpute package surmounts the problem of high-dimensional outcome data by binning genes into smaller groups to analyze pseudo-independently. This method implements covariate MI in gene expression studies by 1) randomly binning genes into smaller groups, 2) creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) estimating gene expression changes using `limma::voom` followed by `limma::lmFit` functions, separately on each M imputed dataset within each gene bin, 4) un-binning the gene sets and stacking the M sets of model results before applying the `limma::squeezeVar` function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) adjusting P-values for multiplicity to account for false discovery rate (FDR). A faster method uses principal component analysis (PCA) to avoid binning genes while still retaining outcome information in the MI models. Binning genes into smaller groups requires that the MI and limma-voom analysis is run many times (typically hundreds). The more computationally efficient MI PCA method implements covariate MI in gene expression studies by 1) performing PCA on the log CPM values for all genes using the Bioconductor `PCAtools` package, 2) creating M imputed datasets where the imputation predictor matrix includes all covariates and the optimum number of PCs to retain (e.g., based on Horn’s parallel analysis or the number of PCs that account for >80% explained variation), 3) conducting the standard limma-voom pipeline with the `voom` followed by `lmFit` followed by `eBayes` functions on each M imputed dataset, 4) pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 5) adjusting P-values for multiplicity to account for false discovery rate (FDR).

Last updated 2 months ago

rnaseqgeneexpressiondifferentialexpressionsequencing

4.48 score 1 stars 6 scripts 106 downloads

gg4way - 4way Plots of Differential Expression

4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.

Last updated 2 months ago

softwarevisualizationdifferentialexpressiongeneexpressiontranscriptionrnaseqsinglecellsequencing

4.48 score 1 scripts 130 downloads

hicVennDiagram - Venn Diagram for genomic interaction data

A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.

Last updated 2 months ago

dna3dstructurehicvisualization

4.48 score 5 scripts 114 downloads

pairedGSEA - Paired DGE and DGS analysis for gene set enrichment analysis

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

Last updated 2 months ago

differentialexpressionalternativesplicingdifferentialsplicinggeneexpressionimmunooncologygenesetenrichmentpathwaysrnaseqsoftwaretranscription

4.48 score 2 stars 110 downloads

SCArray.sat - Large-scale single-cell RNA-seq data analysis using GDS files and Seurat

Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. SCArray.sat introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage without downsampling and can be applied to very large datasets.

Last updated 2 months ago

datarepresentationdataimportsinglecellrnaseq

4.48 score 1 stars 3 scripts 127 downloads

TDbasedUFEadv - Advanced package of tensor decomposition based unsupervised feature extraction

This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.

Last updated 2 months ago

geneexpressionfeatureextractionmethylationarraysinglecellsoftwarebioconductor-packagebioinformaticstensor-decomposition

4.48 score 4 scripts 130 downloads

DNAfusion - Identification of gene fusions using paired-end sequencing

DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.

Last updated 2 months ago

targetedresequencinggeneticsgenefusiondetectionsequencingbioconductor-packagecirculating-tumor-dnagene-fusionliquid-biopsynext-generation-sequencingtargeted-sequencingvariant-calling

4.48 score 3 stars 10 scripts 132 downloads

ccImpute - ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)

Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities.

Last updated 2 months ago

singlecellsequencingprincipalcomponentdimensionreductionclusteringrnaseqtranscriptomicsopenblascppopenmp

4.48 score 2 stars 2 scripts 154 downloads

epistasisGA - An R package to identify multi-snp effects in nuclear family studies using the GADGETS method

This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.

Last updated 2 months ago

geneticssnpgeneticvariabilityopenblascpp

4.48 score 1 stars 5 scripts 118 downloads

seqArchR - Identify Different Architectures of Sequence Elements

seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.

Last updated 2 months ago

motifdiscoverygeneregulationmathematicalbiologysystemsbiologytranscriptomicsgeneticsclusteringdimensionreductionfeatureextractiondnaseqnmfnonnegative-matrix-factorizationpromoter-sequence-architecturesscikit-learnsequence-analysissequence-architecturesunsupervised-machine-learning

4.48 score 1 stars 1 dependents 9 scripts 174 downloads

updateObject - Find/fix old serialized S4 instances

A set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress.

Last updated 2 months ago

infrastructuredatarepresentationbioconductor-packagecore-package

4.48 score 1 stars 3 scripts 98 downloads

mitoClone2 - Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.

Last updated 2 months ago

annotationdataimportgeneticssnpsoftwaresinglecellalignmentcurlbzip2xz-utilszlibcpp

4.48 score 1 stars 8 scripts 204 downloads

BUSseq - Batch Effect Correction with Unknow Subtypes for scRNA-seq data

BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value can be used for downstream analysis as if all cells were sequenced in a single batch. BUSseq can integrate read count matrices obtained from different scRNA-seq platforms and allow cell types to be measured in some but not all of the batches as long as the experimental design fulfills the conditions listed in our manuscript.

Last updated 2 months ago

experimentaldesigngeneexpressionstatisticalmethodbayesianclusteringfeatureextractionbatcheffectsinglecellsequencingcppopenmp

4.48 score 30 scripts 190 downloads

tLOH - Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).

Last updated 2 months ago

copynumbervariationtranscriptionsnpgeneexpressiontranscriptomics

4.48 score 3 stars 4 scripts 134 downloads

granulator - Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data

granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.

Last updated 2 months ago

rnaseqgeneexpressiondifferentialexpressiontranscriptomicssinglecellstatisticalmethodregression

4.48 score 3 stars 6 scripts 258 downloads

treekoR - Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; quantify a cell types as a proportion relative to all cells in a sample (%total), and, as the proportion relative to a parent population (%parent); perform significance testing using the calculated proportions; and provide an interactive html visualisation to help highlight key results.

Last updated 2 months ago

clusteringdifferentialexpressionflowcytometryimmunooncologymassspectrometrysinglecellsoftwarestatisticalmethodvisualization

4.48 score 1 dependents 10 scripts 164 downloads

LRcell - Differential cell type change analysis using Logistic/linear Regression

The goal of LRcell is to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. To achieve this, LRcell utilizes sets of cell marker genes acquired from single-cell RNA-sequencing (scRNA-seq) as indicators for various cell types in the tissue of interest. Next, for each cell type, using its marker genes as indicators, we apply Logistic Regression on the complete set of genes with differential expression p-values to calculate a cell-type significance p-value. Finally, these p-values are compared to predict which one(s) are likely to be responsible for the differential gene expression pattern observed in the bulk RNA-seq experiments. LRcell is inspired by the LRpath[@sartor2009lrpath] algorithm developed by Sartor et al., originally designed for pathway/gene set enrichment analysis. LRcell contains three major components: LRcell analysis, plot generation and marker gene selection. All modules in this package are written in R. This package also provides marker genes in the Prefrontal Cortex (pFC) human brain region, human PBMC and nine mouse brain regions (Frontal Cortex, Cerebellum, Globus Pallidus, Hippocampus, Entopeduncular, Posterior Cortex, Striatum, Substantia Nigra and Thalamus).

Last updated 2 months ago

singlecellgenesetenrichmentsequencingregressiongeneexpressiondifferentialexpressionenrichmentmarker-genes

4.48 score 3 stars 5 scripts 139 downloads

ComPrAn - Complexome Profiling Analysis package

This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.

Last updated 2 months ago

massspectrometryproteomicsvisualization

4.48 score 5 scripts 140 downloads

ORFhunteR - Predict open reading frames in nucleotide sequences

The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells.

Last updated 2 months ago

technologystatisticalmethodsequencingrnaseqclassificationfeatureextraction

4.48 score 1 stars 138 downloads

RLassoCox - A reweighted Lasso-Cox by integrating gene interaction information

RLassoCox is a package that implements the RLasso-Cox model proposed by Wei Liu. The RLasso-Cox model integrates gene interaction information into the Lasso-Cox model for accurate survival prediction and survival biomarker discovery. It is based on the hypothesis that topologically important genes in the gene interaction network tend to have stable expression changes. The RLasso-Cox model uses random walk to evaluate the topological weight of genes, and then highlights topologically important genes to improve the generalization ability of the Lasso-Cox model. The RLasso-Cox model has the advantage of identifying small gene sets with high prognostic performance on independent datasets, which may play an important role in identifying robust survival biomarkers for various cancer types.

Last updated 2 months ago

survivalregressiongeneexpressiongenepredictionnetwork

4.48 score 3 stars 2 scripts 157 downloads

SCFA - SCFA: Subtyping via Consensus Factor Analysis

Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in multi-omics data. SCFA first uses an autoencoder to select only important features and then repeatedly performs factor analysis to represent the data with different numbers of factors. Using these representations, it can reliably identify cancer subtypes and accurately predict risk scores of patients.

Last updated 2 months ago

survivalclusteringclassification

4.48 score 3 stars 2 scripts 122 downloads

AnVILPublish - Publish Packages and Other Resources to AnVIL Workspaces

Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the 'DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.

Last updated 2 months ago

infrastructuresoftware

4.48 score 204 downloads

rnaEditr - Statistical analysis of RNA editing sites and hyper-editing regions

RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

Last updated 2 months ago

genetargetepigeneticsdimensionreductionfeatureextractionregressionsurvivalrnaseq

4.48 score 3 stars 9 scripts 182 downloads

uncoverappLib - Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.

Last updated 2 months ago

softwarevisualizationannotationcoverage

4.48 score 3 stars 4 scripts 188 downloads

combi - Compositional omics model based visual integration

This explorative ordination method combines quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration are available. The results are shown as interpretable, compositional multiplots.

Last updated 2 months ago

metagenomicsdimensionreductionmicrobiomevisualizationmetabolomics

4.48 score 1 stars 7 scripts 190 downloads

biobtreeR - Using biobtree tool from R

The biobtreeR package provides an interface to [biobtree](https://github.com/tamerh/biobtree) tool which covers large set of bioinformatics datasets and allows search and chain mappings functionalities.

Last updated 2 months ago

annotationbioinformatics

4.48 score 3 stars 3 scripts 246 downloads

MACSQuantifyR - Fast treatment of MACSQuantify FACS data

Automatically process the metadata of MACSQuantify FACS sorter. It runs multiple modules: i) imports of raw file and graphical selection of duplicates in well plate, ii) computes statistics on data and iii) can compute combination index.

Last updated 2 months ago

dataimportpreprocessingnormalizationflowcytometrydatarepresentationgui

4.48 score 3 scripts 121 downloads

microbiomeDASim - Microbiome Differential Abundance Simulation

A toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance.

Last updated 2 months ago

microbiomevisualizationsoftware

4.48 score 3 stars 1 scripts 172 downloads

HiCBricks - Framework for Storing and Accessing Hi-C Data Through HDF Files

HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.

Last updated 2 months ago

dataimportinfrastructuresoftwaretechnologysequencinghic

4.48 score 1 dependents 9 scripts 278 downloads

transite - RNA-binding protein motif analysis

transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.

Last updated 2 months ago

geneexpressiontranscriptiondifferentialexpressionmicroarraymrnamicroarraygeneticsgenesetenrichmentcpp

4.48 score 20 scripts 215 downloads

Rtpca - Thermal proximity co-aggregation with R

R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions.

Last updated 2 months ago

softwareproteomicsdataimport

4.46 score 29 scripts 190 downloads

DelayedRandomArray - Delayed Arrays of Random Values

Implements a DelayedArray of random values where the realization of the sampled values is delayed until they are needed. Reproducible sampling within any subarray is achieved by chunking where each chunk is initialized with a different random seed and stream. The usual distributions in the stats package are supported, along with scalar, vector and arrays for the parameters.

Last updated 2 months ago

datarepresentationcpp

4.43 score 1 dependents 6 scripts 133 downloads

MMUPHin - Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery.

Last updated 2 months ago

metagenomicsmicrobiomebatcheffect

4.43 score 45 scripts 409 downloads

graper - Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes

This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach.

Last updated 2 months ago

regressionbayesianclassification

4.41 score 13 scripts 147 downloads

PoDCall - Positive Droplet Calling for DNA Methylation Droplet Digital PCR

Reads files exported from 'QX Manager or QuantaSoft' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

Last updated 3 days ago

classificationepigeneticsddpcrdifferentialmethylationcpgislanddnamethylation

4.40 score 5 scripts 116 downloads

EpipwR - Efficient Power Analysis for EWAS with Continuous or Binary Outcomes

A quasi-simulation based approach to performing power analysis for EWAS (Epigenome-wide association studies) with continuous or binary outcomes. 'EpipwR' relies on empirical EWAS datasets to determine power at specific sample sizes while keeping computational cost low. EpipwR can be run with a variety of standard statistical tests, controlling for either a false discovery rate or a family-wise type I error rate.

Last updated 2 months ago

epigeneticsexperimentaldesign

4.40 score 3 scripts

ggseqalign - Minimal Visualization of Sequence Alignments

Simple visualizations of alignments of DNA or AA sequences as well as arbitrary strings. Compatible with Biostrings and ggplot2. The plots are fully customizable using ggplot2 modifiers such as theme().

Last updated 2 months ago

alignmentmultiplesequencealignmentsoftwarevisualizationbioinformaticsggplot2-enhancementsminimalistic

4.40 score 118 downloads

tidyFlowCore - tidyFlowCore: Bringing flowCore to the tidyverse

tidyFlowCore bridges the gap between flow cytometry analysis using the flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame and flowSet objects as if they were tibbles; however, your data remain flowCore data structures under this layer of abstraction. tidyFlowCore enables intuitive and streamlined analysis workflows that can leverage both the Bioconductor and tidyverse ecosystems for cytometry data.

Last updated 2 months ago

singlecellflowcytometryinfrastructure

4.40 score 1 stars 7 scripts 76 downloads

BREW3R.r - R package associated to BREW3R

This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.

Last updated 2 months ago

genomeannotation

4.40 score 6 scripts 130 downloads

biocroxytest - Handle Long Tests in Bioconductor Packages

This package provides a roclet for roxygen2 that identifies and processes code blocks in your documentation marked with `@longtests`. These blocks should contain tests that take a long time to run and thus cannot be included in the regular test suite of the package. When you run `roxygen2::roxygenise` with the `longtests_roclet`, it will extract these long tests from your documentation and save them in a separate directory. This allows you to run these long tests separately from the rest of your tests, for example, on a continuous integration server that is set up to run long tests.

Last updated 2 months ago

softwareinfrastructure

4.40 score 1 stars 3 scripts 134 downloads

saseR - Scalable Aberrant Splicing and Expression Retrieval

saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: \itemize{ \item \code{\link{BamtoAspliCounts}} - Process BAM files to ASpli counts \item \code{\link{convertASpli}} - Get gene, bin or junction counts from ASpli SummarizedExperiment \item \code{\link{calculateOffsets}} - Create an offsets assays for aberrant expression or splicing analysis \item \code{\link{saseRfindEncodingDim}} - Estimate the optimal number of latent factors to include when estimating the mean expression \item \code{\link{saseRfit}} - Parameter estimation of the negative binomial distribution and compute p-values for aberrant expression and splicing } For information upon how to use these functions, check out our vignette at \url{https://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd} and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRxiv. \url{https://doi.org/10.1101/2023.06.29.547014}.

Last updated 2 months ago

differentialexpressiondifferentialsplicingregressiongeneexpressionalternativesplicingrnaseqsequencingsoftware

4.40 score 1 stars 1 scripts 122 downloads

SpatialOmicsOverlay - Spatial Overlay for Omic Data from Nanostring GeoMx Data

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

Last updated 2 months ago

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk

4.40 score 8 scripts 176 downloads

CircSeqAlignTk - A toolkit for end-to-end analysis of RNA-seq data for circular genomes

CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.

Last updated 2 months ago

sequencingsmallrnaalignmentsoftware

4.40 score 3 scripts 145 downloads

phenomis - Postprocessing and univariate analysis of omics data

The 'phenomis' package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the 'ropls' and 'biosigner' packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).

Last updated 2 months ago

batcheffectclusteringcoveragekeggmassspectrometrymetabolomicsnormalizationproteomicsqualitycontrolsequencingstatisticalmethodtranscriptomics

4.40 score 6 scripts 179 downloads

EasyCellType - Annotate cell types for scRNA-seq data

We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.

Last updated 2 months ago

singlecellsoftwaregeneexpressiongenesetenrichment

4.40 score 6 scripts 180 downloads

chihaya - Save Delayed Operations to a HDF5 File

Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray's contents in other languages and analysis frameworks.

Last updated 2 months ago

dataimportdatarepresentationzlibcpp

4.38 score 16 scripts 250 downloads

CTSV - Identification of cell-type-specific spatially variable genes accounting for excess zeros

The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.

Last updated 2 months ago

geneexpressionstatisticalmethodregressionspatialgenetics

4.38 score 2 stars 12 scripts 164 downloads

flowSpecs - Tools for processing of high-dimensional cytometry data

This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.

Last updated 2 months ago

softwarecellbasedassaysdatarepresentationimmunooncologyflowcytometrysinglecellvisualizationnormalizationdataimport

4.38 score 6 stars 7 scripts 224 downloads

qckitfastq - FASTQ Quality Control

Assessment of FASTQ file format with multiple metrics including quality score, sequence content, overrepresented sequence and Kmers.

Last updated 2 months ago

softwarequalitycontrolsequencingzlibcpp

4.38 score 24 scripts 180 downloads

Qtlizer - Comprehensive QTL annotation of GWAS results

This R package provides access to the Qtlizer web server. Qtlizer annotates lists of common small variants (mainly SNPs) and genes in humans with associated changes in gene expression using the most comprehensive database of published quantitative trait loci (QTLs).

Last updated 2 months ago

genomewideassociationsnpgeneticslinkagedisequilibriumeqtlgwasvariant-annotation

4.38 score 3 stars 2 scripts 144 downloads

DepInfeR - Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out preprint on bioRxiv: https://doi.org/10.1101/2022.01.11.475864.

Last updated 2 months ago

softwareregressionpharmacogeneticspharmacogenomicsfunctionalgenomics

4.36 score 1 stars 23 scripts 121 downloads

ASURAT - Functional annotation-driven unsupervised clustering for single-cell data

ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

Last updated 2 months ago

geneexpressionsinglecellsequencingclusteringgenesignalingcpp

4.36 score 23 scripts 139 downloads

ToxicoGx - Analysis of Large-Scale Toxico-Genomic Data

Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.

Last updated 2 months ago

geneexpressionpharmacogeneticspharmacogenomicssoftware

4.36 score 23 scripts 194 downloads

ggmanh - Visualization Tool for GWAS Result

Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

Last updated 2 months ago

visualizationgenomewideassociationgenetics

4.34 score 22 scripts 441 downloads

drugTargetInteractions - Drug-Target Interactions

Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.

Last updated 2 months ago

cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsproteomicsmetabolomics

4.34 score 1 stars 11 scripts 142 downloads

ROSeq - Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data

ROSeq - A rank based approach to modeling gene expression with filtered and normalized read count matrix. ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially expressed genes between the contrasting groups of single cells. One of the input parameters is the number of cores to be used.

Last updated 2 months ago

geneexpressiondifferentialexpressionsinglecellcount-datagene-expressiongene-expression-profilesnormalizationpopulationsranktmmtungtung-datasettutorialvignette

4.34 score 2 stars 11 scripts 188 downloads

Spaniel - Spatial Transcriptomics Analysis

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.

Last updated 2 months ago

singlecellrnaseqqualitycontrolpreprocessingnormalizationvisualizationtranscriptomicsgeneexpressionsequencingsoftwaredataimportdatarepresentationinfrastructurecoverageclustering

4.34 score 22 scripts 174 downloads

pareg - Pathway enrichment using a regularized regression approach

Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.

Last updated 5 days ago

softwarestatisticalmethodgraphandnetworkregressiongeneexpressiondifferentialexpressionnetworkenrichmentnetwork

4.32 score 7 stars 4 scripts 160 downloads

IFAA - Robust Inference for Absolute Abundance in Microbiome Analysis

This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal to the ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the 'MZILN' function for estimating and testing associations of abundance ratios with covariates.

Last updated 2 months ago

softwaretechnologysequencingmicrobiomeregression

4.32 score 14 scripts 122 downloads

PDATK - Pancreatic Ductal Adenocarcinoma Tool-Kit

Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) [https://doi.org/10.1200/cci.18.00102] and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.

Last updated 2 months ago

geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationsurvivalclusteringgeneprediction

4.31 score 1 stars 17 scripts 372 downloads

DuplexDiscovereR - Analysis of the data from RNA duplex probing experiments

DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.

Last updated 2 months ago

sequencingtranscriptomicsstructuralpredictionclusteringsplicedalignment

4.30 score 1 stars 5 scripts 53 downloads

RNAdecay - Maximum Likelihood Decay Modeling of RNA Degradation Data

RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: functions are provided to easily visualize decay data model, or half-life distributions using ggplot2 package functions.

Last updated 2 months ago

immunooncologysoftwaregeneexpressiongeneregulationdifferentialexpressiontranscriptiontranscriptomicstimecourseregressionrnaseqnormalizationworkflowstep

4.30 score 2 scripts 160 downloads

MSstatsBig - MSstats Preprocessing for Larger than Memory Data

MSstats package provide tools for preprocessing, summarization and differential analysis of mass spectrometry (MS) proteomics data. Recently, some MS protocols enable acquisition of data sets that result in larger than memory quantitative data. MSstats functions are not able to process such data. MSstatsBig package provides additional converter functions that enable processing larger than memory data sets.

Last updated 2 months ago

massspectrometryproteomicssoftware

4.30 score 1 scripts 106 downloads

MICSQTL - MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)

Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.

Last updated 2 months ago

geneexpressiongeneticsproteomicsrnaseqsequencingsinglecellsoftwarevisualizationcellbasedassayscoverage

4.30 score 3 scripts 112 downloads

FeatSeekR - FeatSeekR an R package for unsupervised feature selection

FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness.

Last updated 2 months ago

softwarestatisticalmethodfeatureextractionmassspectrometry

4.30 score 2 stars 3 scripts 112 downloads

cytofQC - Labels normalized cells for CyTOF data and assigns probabilities for each label

cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.

Last updated 2 months ago

softwaresinglecellannotation

4.30 score 2 stars 3 scripts 170 downloads

HiCool - HiCool

HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

Last updated 2 months ago

hicdna3dstructuredataimport

4.30 score 2 stars 10 scripts 148 downloads

microSTASIS - Microbiota STability ASsessment via Iterative cluStering

The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

Last updated 2 months ago

geneticvariabilitybiomedicalinformaticsclusteringmultiplecomparisonmicrobiome

4.30 score 2 stars 1 scripts 118 downloads

ggtreeDendro - Drawing 'dendrogram' using 'ggtree'

Offers a set of 'autoplot' methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using 'ggtree'. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree.

Last updated 2 months ago

clusteringclassificationdecisiontreephylogeneticsvisualization

4.30 score 7 scripts 130 downloads

consICA - consensus Independent Component Analysis

consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems.

Last updated 2 months ago

technologystatisticalmethodsequencingrnaseqtranscriptomicsclassificationfeatureextraction

4.30 score 362 downloads

regioneReloaded - RegioneReloaded: Multiple Association for Genomic Region Sets

RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

Last updated 2 months ago

geneticschipseqdnaseqmethylseqcopynumbervariationclusteringmultiplecomparison

4.30 score 5 stars 2 scripts 164 downloads

crisprBwa - BWA-based alignment of CRISPR gRNA spacer sequences

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.

Last updated 2 months ago

crisprfunctionalgenomicsalignmentalignerbioconductorbioconductor-packagebwacrispr-analysiscrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequencessgrnasgrna-design

4.30 score 1 stars 6 scripts 162 downloads

GenomicInteractionNodes - A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

The GenomicInteractionNodes package can import interactions from bedpe file and define the interaction nodes, the genomic interaction sites with multiple interaction loops. The interaction nodes is a binding platform regulates one or multiple genes. The detected interaction nodes will be annotated for downstream validation.

Last updated 2 months ago

hicsequencingsoftware

4.30 score 1 scripts 125 downloads

qmtools - Quantitative Metabolomics Data Processing Tools

The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.

Last updated 2 months ago

metabolomicspreprocessingnormalizationdimensionreductionmassspectrometry

4.30 score 1 stars 5 scripts 131 downloads

protGear - Protein Micro Array Data Management and Interactive Visualization

A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

Last updated 2 months ago

microarrayonechannelpreprocessingbiomedicalinformaticsproteomicsbatcheffectnormalizationbayesianclusteringregressionsystemsbiologyimmunooncologybackground-correctionmicroarray-datanormalisationproteomics-datashinyshinydashboard

4.30 score 1 stars 6 scripts 258 downloads

GenProSeq - Generating Protein Sequences with Deep Generative Models

Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. Machine learning has enabled us to generate useful protein sequences on a variety of scales. Generative models are machine learning methods which seek to model the distribution underlying the data, allowing for the generation of novel samples with similar properties to those on which the model was trained. Generative models of proteins can learn biologically meaningful representations helpful for a variety of downstream tasks. Furthermore, they can learn to generate protein sequences that have not been observed before and to assign higher probability to protein sequences that satisfy desired criteria. In this package, common deep generative models for protein sequences, such as variational autoencoder (VAE), generative adversarial networks (GAN), and autoregressive models are available. In the VAE and GAN, the Word2vec is used for embedding. The transformer encoder is applied to protein sequences for the autoregressive model.

Last updated 2 months ago

softwareproteomicsopenjdk

4.30 score 3 scripts 132 downloads

biodbHmdb - biodbHmdb, a library for connecting to the HMDB Database

The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.

Last updated 2 months ago

softwareinfrastructuredataimportcpp

4.30 score 2 stars 2 scripts 170 downloads

txcutr - Transcriptome CUTteR

Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.

Last updated 2 months ago

alignmentannotationrnaseqsequencingtranscriptomics

4.30 score 9 scripts 134 downloads

mosbi - Molecular Signature identification using Biclustering

This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.

Last updated 2 months ago

softwarestatisticalmethodclusteringnetwork

4.30 score 8 scripts 138 downloads

biodbUniprot - biodbUniprot, a library for connecting to the Uniprot Database

The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for searching for entries.

Last updated 2 months ago

softwareinfrastructuredataimport

4.30 score 2 stars 3 scripts 121 downloads

spatzie - Identification of enriched motif pairs from chromatin interaction data

Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.

Last updated 2 months ago

dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhictranscription

4.30 score 5 scripts 130 downloads

cageminer - Candidate Gene Miner

This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.

Last updated 2 months ago

softwaresnpfunctionalpredictiongenomewideassociationgeneexpressionnetworkenrichmentvariantannotationfunctionalgenomicsnetwork

4.30 score 1 stars 2 scripts 139 downloads

m6Aboost - m6Aboost

This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.

Last updated 2 months ago

sequencingepigeneticsgeneticsexperimenthubsoftware

4.30 score 2 stars 5 scripts 132 downloads

MSstatsLOBD - Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) <doi:10.1074/mcp.RA117.000322>.

Last updated 2 months ago

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolmass-spectrometry

4.30 score 1 scripts 140 downloads

BloodGen3Module - This R package for performing module repertoire analyses and generating fingerprint representations

The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.1101/525709v2 and https://pubmed.ncbi.nlm.nih.gov/33624743/, the results of module repertoire analyses can be represented in a fingerprint format, where red and blue spots indicate increases or decreases in module activity. These spots are subsequently represented either on a grid, with each position being assigned to a given module, or in a heatmap where the samples are arranged in columns and the modules in rows.

Last updated 2 months ago

softwarevisualizationgeneexpression

4.30 score 4 scripts 248 downloads

wppi - Weighting protein-protein interactions

Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.

Last updated 2 months ago

graphandnetworknetworkpathwayssoftwaregenesignalinggenetargetsystemsbiologytranscriptomicsannotationgene-ontologygene-prioritizationhuman-phenotype-ontologyomnipathppi-networksrandom-walk-with-restart

4.30 score 1 stars 4 scripts 204 downloads

cyanoFilter - Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.

Last updated 2 months ago

flowcytometryclusteringonechannel

4.30 score 4 scripts 248 downloads

CIMICE - CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction.

Last updated 2 months ago

softwarebiologicalquestionnetworkinferenceresearchfieldphylogeneticsstatisticalmethodgraphandnetworktechnologysinglecell

4.30 score 5 scripts 130 downloads

geva - Gene Expression Variation Analysis (GEVA)

Statistic methods to evaluate variations of differential expression (DE) between multiple biological conditions. It takes into account the fold-changes and p-values from previous differential expression (DE) results that use large-scale data (*e.g.*, microarray and RNA-seq) and evaluates which genes would react in response to the distinct experiments. This evaluation involves an unique pipeline of statistical methods, including weighted summarization, quantile detection, cluster analysis, and ANOVA tests, in order to classify a subset of relevant genes whose DE is similar or dependent to certain biological factors.

Last updated 2 months ago

classificationdifferentialexpressiongeneexpressionmicroarraymultiplecomparisonrnaseqsystemsbiologytranscriptomics

4.30 score 2 stars 4 scripts 132 downloads

MACSr - MACS: Model-based Analysis for ChIP-Seq

The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

Last updated 2 months ago

softwarechipseqatacseqimmunooncology

4.30 score 7 scripts 268 downloads

censcyt - Differential abundance analysis with a right censored covariate in high-dimensional cytometry

Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.

Last updated 2 months ago

immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftwaresurvival

4.30 score 2 scripts 151 downloads

ADImpute - Adaptive Dropout Imputer (ADImpute)

Single-cell RNA sequencing (scRNA-seq) methods are typically unable to quantify the expression levels of all genes in a cell, creating a need for the computational prediction of missing values (‘dropout imputation’). Most existing dropout imputation methods are limited in the sense that they exclusively use the scRNA-seq dataset at hand and do not exploit external gene-gene relationship information. Here we propose two novel methods: a gene regulatory network-based approach using gene-gene relationships learnt from external data and a baseline approach corresponding to a sample-wide average. ADImpute can implement these novel methods and also combine them with existing imputation methods (currently supported: DrImpute, SAVER). ADImpute can learn the best performing method per gene and combine the results from different methods into an ensemble.

Last updated 2 months ago

geneexpressionnetworkpreprocessingsequencingsinglecelltranscriptomics

4.30 score 7 scripts 355 downloads

AnVILBilling - Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).

AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.

Last updated 2 months ago

infrastructuresoftware

4.30 score 5 scripts 140 downloads

gmoviz - Seamless visualization of complex genomic variations in GMOs and edited cell lines

Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.

Last updated 2 months ago

visualizationsequencinggeneticvariabilitygenomicvariationcoverage

4.30 score 9 scripts 139 downloads

CeTF - Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network and can be applied to any correlation-based network including but not limited to gene co-expression networks, while the RIF algorithm identify critical Transcription Factors (TF) from gene expression data. These two algorithms when combined provide a very relevant layer of information for gene expression studies (Microarray, RNA-seq and single-cell RNA-seq data).

Last updated 2 months ago

sequencingrnaseqmicroarraygeneexpressiontranscriptionnormalizationdifferentialexpressionsinglecellnetworkregressionchipseqimmunooncologycoveragecpp

4.30 score 8 scripts 199 downloads

PathNet - An R package for pathway analysis using topological information

PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.

Last updated 2 months ago

pathwaysdifferentialexpressionmultiplecomparisonkeggnetworkenrichmentnetwork

4.30 score 5 scripts 229 downloads

oppti - Outlier Protein and Phosphosite Target Identifier

The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets.

Last updated 2 months ago

proteomicsregressiondifferentialexpressionbiomedicalinformaticsgenetargetgeneexpressionnetwork

4.30 score 2 stars 2 scripts 132 downloads

blacksheepr - Outlier Analysis for pairwise differential comparison

Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics or transcriptomics, but it can be used for any data that can be represented by a 2D table, and has two sub populations within the table to compare.

Last updated 2 months ago

sequencingrnaseqgeneexpressiontranscriptiondifferentialexpressiontranscriptomics

4.30 score 6 scripts 198 downloads

idr2d - Irreproducible Discovery Rate for Genomic Interactions Data

A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks.

Last updated 2 months ago

dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhic

4.30 score 6 scripts 148 downloads

SigsPack - Mutational Signature Estimation for Single Samples

Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues.

Last updated 2 months ago

somaticmutationsnpvariantannotationbiomedicalinformaticsdnaseq

4.30 score 2 stars 4 scripts 163 downloads

scBFA - A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq

This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis.

Last updated 2 months ago

singlecelltranscriptomicsdimensionreductiongeneexpressionatacseqbatcheffectkeggqualitycontrol

4.30 score 4 scripts 176 downloads

GOTHiC - Binomial test for Hi-C data analysis

This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.

Last updated 2 months ago

immunooncologysequencingpreprocessingepigeneticshic

4.30 score 6 scripts 233 downloads

RNAmodR.AlkAnilineSeq - Detection of m7G, m3C and D modification by AlkAnilineSeq

RNAmodR.AlkAnilineSeq implements the detection of m7G, m3C and D modifications on RNA from experimental data generated with the AlkAnilineSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

Last updated 2 months ago

softwareworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsrnarnamodr

4.30 score 2 stars 3 scripts 163 downloads

SynMut - SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It is a powerful tool for in silico designs of DNA sequence mutants.

Last updated 2 months ago

sequencematchingexperimentaldesignpreprocessing

4.30 score 2 stars 1 scripts 156 downloads

SpatialCPie - Cluster analysis of Spatial Transcriptomics data

SpatialCPie is an R package designed to facilitate cluster evaluation for spatial transcriptomics data by providing intuitive visualizations that display the relationships between clusters in order to guide the user during cluster identification and other downstream applications. The package is built around a shiny "gadget" to allow the exploration of the data with multiple plots in parallel and an interactive UI. The user can easily toggle between different cluster resolutions in order to choose the most appropriate visual cues.

Last updated 2 months ago

transcriptomicsclusteringrnaseqsoftware

4.30 score 2 scripts 198 downloads

DNABarcodeCompatibility - A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

The package allows one to obtain optimised combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimiser function to further favor the selection of barcode combinations with least heterogeneity in barcode usage.

Last updated 2 months ago

preprocessingsequencingcpp

4.30 score 2 scripts 114 downloads

scDDboost - A compositional model to assess expression changes from single-cell rna-seq data

scDDboost is an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions. Compared to other methods that assess differential expression, scDDboost benefits uniquely from information conveyed by the clustering of cells into cellular subtypes. Through a novel empirical Bayesian formulation it calculates gene-specific posterior probabilities that the marginal expression distribution is the same (or different) between the two conditions. The implementation in scDDboost treats gene-level expression data within each condition as a mixture of negative binomial distributions.

Last updated 2 months ago

singlecellsoftwareclusteringsequencinggeneexpressiondifferentialexpressionbayesiancpp

4.28 score 19 scripts 162 downloads

cliProfiler - A package for the CLIP data visualization

An easy and fast way to visualize and profile the high-throughput IP data. This package generates the meta gene profile and other profiles. These profiles could provide valuable information for understanding the IP experiment results.

Last updated 2 months ago

sequencingchipseqvisualizationepigeneticsgenetics

4.28 score 19 scripts 126 downloads

Rbwa - R wrapper for BWA-backtrack and BWA-MEM aligners

Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

Last updated 2 months ago

sequencingalignmentbwabwa-memdna-sequencesdna-sequencing

4.26 score 1 dependents 10 scripts 154 downloads

MEIGOR - MEIGOR - MEtaheuristics for bIoinformatics Global Optimization

MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow.

Last updated 2 months ago

systemsbiologyoptimizationsoftware

4.25 score 44 scripts 214 downloads

scHOT - single-cell higher order testing

Single cell Higher Order Testing (scHOT) is an R package that facilitates testing changes in higher order structure of gene expression along either a developmental trajectory or across space. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data.

Last updated 2 months ago

geneexpressionrnaseqsequencingsinglecellsoftwaretranscriptomics

4.23 score 17 scripts 162 downloads

HarmonizR - Handles missing values and makes more data available

An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.

Last updated 2 months ago

batcheffect

4.20 score 16 scripts 134 downloads

mastR - Markers Automated Screening Tool in R

mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.

Last updated 2 months ago

softwaregeneexpressiontranscriptomicsdifferentialexpressionvisualization

4.20 score 4 stars 3 scripts 370 downloads

easier - Estimate Systems Immune Response from RNA-seq data

This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.

Last updated 2 months ago

geneexpressionsoftwaretranscriptionsystemsbiologypathwaysgenesetenrichmentimmunooncologyepigeneticsclassificationbiomedicalinformaticsregressionexperimenthubsoftware

4.20 score 16 scripts 222 downloads

TreeAndLeaf - Displaying binary trees with focus on dendrogram leaves

The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves.

Last updated 2 months ago

infrastructuregraphandnetworksoftwarenetworkvisualizationdatarepresentation

4.20 score 16 scripts 272 downloads

TPP2D - Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.

Last updated 2 months ago

softwareproteomicsdataimport

4.20 score 16 scripts 149 downloads

InPAS - Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.

Last updated 2 days ago

alternative polyadenylationdifferential polyadenylation site usagerna-seqgene regulationtranscription

4.18 score 1 scripts 258 downloads

betaHMM - A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

A novel approach utilizing a homogeneous hidden Markov model. And effectively model untransformed beta values. To identify DMCs while considering the spatial. Correlation of the adjacent CpG sites.

Last updated 4 days ago

dnamethylationdifferentialmethylationimmunooncologybiomedicalinformaticsmethylationarraysoftwaremultiplecomparisonsequencingspatialcoveragegenetargethiddenmarkovmodelmicroarray

4.18 score 106 downloads

spatialSimGP - Simulate Spatial Transcriptomics Data with the Mean-variance Relationship

This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene.

Last updated 2 months ago

spatialtranscriptomicsgeneexpression

4.18 score 2 scripts

Rvisdiff - Interactive Graphs for Differential Expression

Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.

Last updated 2 months ago

softwarevisualizationrnaseqdatarepresentationdifferentialexpression

4.18 score 2 scripts 128 downloads

HERON - Hierarchical Epitope pROtein biNding

HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.

Last updated 2 months ago

microarraysoftware

4.18 score 1 stars 6 scripts 112 downloads

partCNV - Infer locally aneuploid cells using single cell RNA-seq data

This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).

Last updated 2 months ago

softwarecopynumbervariationhiddenmarkovmodelsinglecellclassification

4.18 score 4 scripts 114 downloads

MultimodalExperiment - Integrative Bulk and Single-Cell Experiment Container

MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.

Last updated 2 months ago

datarepresentationinfrastructuresinglecell

4.18 score 3 scripts 108 downloads

OutSplice - Comparison of Splicing Events between Tumor and Normal Samples

An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.

Last updated 2 months ago

alternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressionrnaseqsoftwarevariantannotation

4.18 score 1 stars 4 scripts 106 downloads

alabaster - Umbrella for the Alabaster Framework

Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.

Last updated 2 months ago

datarepresentationdataimport

4.18 score 3 scripts 144 downloads

BG2 - Performs Bayesian GWAS analysis for non-Gaussian data using BG2

This package is built to perform GWAS analysis for non-Gaussian data using BG2. The BG2 method uses penalized quasi-likelihood along with nonlocal priors in a two step manner to identify SNPs in GWAS analysis. The research related to this package was supported in part by National Science Foundation awards DMS 1853549 and DMS 2054173.

Last updated 2 months ago

bayesianassaydomainsnpgenomewideassociation

4.18 score 3 scripts 144 downloads

metabinR - Abundance and Compositional Based Binning of Metagenomes

Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution.

Last updated 2 months ago

classificationclusteringmicrobiomesequencingsoftwareopenjdk

4.18 score 2 scripts 108 downloads

octad - Open Cancer TherApeutic Discovery (OCTAD)

OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.

Last updated 2 months ago

classificationgeneexpressionpharmacogeneticspharmacogenomicssoftwaregenesetenrichment

4.18 score 4 scripts 141 downloads

ISLET - Individual-Specific ceLl typE referencing Tool

ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.

Last updated 2 months ago

softwarernaseqtranscriptomicstranscriptionsequencinggeneexpressiondifferentialexpressiondifferentialmethylation

4.18 score 9 scripts 158 downloads

ATACseqTFEA - Transcription Factor Enrichment Analysis for ATAC-seq

Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.

Last updated 2 months ago

sequencingdnaseqatacseqmnaseseqgeneregulation

4.18 score 4 scripts 144 downloads

GenomAutomorphism - Compute the automorphisms between DNA's Abelian group representations

This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.

Last updated 2 months ago

mathematicalbiologycomparativegenomicsfunctionalgenomicsmultiplesequencealignmentwholegenomegenetic-codegenetic-code-algebragenomegenome-algebra

4.18 score 3 scripts 102 downloads

cytoMEM - Marker Enrichment Modeling (MEM)

MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features' levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry, mass cytometry, single cell RNA-seq, and spectral flow cytometry using RMSD.

Last updated 2 months ago

proteomicssystemsbiologyclassificationflowcytometrydatarepresentationdataimportcellbiologysinglecellclustering

4.18 score 15 scripts 199 downloads

tomoseqr - R Package for Analyzing Tomo-seq Data

`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.

Last updated 2 months ago

geneexpressionsequencingrnaseqtranscriptomicsspatialvisualizationsoftware

4.18 score 15 scripts 131 downloads

LinTInd - Lineage tracing by indels

When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to reference sequence and generate scar form strings respectively. IndelIdents() function will help you to define a scar form for each cell or read. IndelPlot() function will help you to visualize the distribution of deletion and insertion. TagProcess() function will help you to extract indels for each cell or read. TagDist() function will help you to calculate the similarity between each pair of groups across the indwells they contain. BuildTree() function will help you to reconstruct a tree. PlotTree() function will help you to visualize the tree.

Last updated 2 months ago

singlecellcrispralignment

4.18 score 2 scripts 134 downloads

XNAString - Efficient Manipulation of Modified Oligonucleotide Sequences

The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings and pwalign packages.

Last updated 2 months ago

sequencematchingalignmentsequencinggeneticscpp

4.18 score 4 scripts 136 downloads

HiCDCPlus - Hi-C Direct Caller Plus

Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw contact matrix for each chromosome up to a specified genomic distance, binned by uniform genomic intervals or restriction enzyme fragments, by training a background model to account for random polymer ligation and systematic sources of read count variation.

Last updated 2 months ago

hicdna3dstructuresoftwarenormalizationzlibcpp

4.18 score 15 scripts 215 downloads

GSgalgoR - An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

A multi-objective optimization algorithm for disease sub-type discovery based on a non-dominated sorting genetic algorithm. The 'Galgo' framework combines the advantages of clustering algorithms for grouping heterogeneous 'omics' data and the searching properties of genetic algorithms for feature selection. The algorithm search for the optimal number of clusters determination considering the features that maximize the survival difference between sub-types while keeping cluster consistency high.

Last updated 2 months ago

geneexpressiontranscriptionclusteringclassificationsurvival

4.18 score 15 stars 6 scripts 154 downloads

netboost - Network Analysis Supported by Boosting

Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein.

Last updated 2 months ago

softwarestatisticalmethodgraphandnetworknetworkclusteringdimensionreductionbiomedicalinformaticsepigeneticsmetabolomicstranscriptomicscpp

4.18 score 1 scripts 136 downloads

pram - Pooling RNA-seq datasets for assembling transcript models

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

Last updated 2 months ago

softwaretechnologysequencingrnaseqbiologicalquestiongenepredictiongenomeannotationresearchfieldtranscriptomicsbioconductor-packagegenome-annotationrna-seqtranscript-model

4.18 score 1 stars 3 scripts 178 downloads

scTensor - Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.

Last updated 2 months ago

dimensionreductionsinglecellsoftwaregeneexpression

4.18 score 2 scripts 222 downloads

AssessORF - Assess Gene Predictions Using Proteomics and Evolutionary Conservation

In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomic hits and evolutionarily conserved start codons as the forms of evidence.

Last updated 2 months ago

comparativegenomicsgenepredictiongenomeannotationgeneticsproteomicsqualitycontrolvisualization

4.18 score 3 scripts 458 downloads

OmicsMLRepoR - Search harmonized metadata created under the OmicsMLRepo project

This package provides functions to browse the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology.

Last updated 2 months ago

softwareinfrastructuredatarepresentation

4.17 score 14 scripts

LoomExperiment - LoomExperiment container

The LoomExperiment package provide a means to easily convert the Bioconductor "Experiment" classes to loom files and vice versa.

Last updated 2 months ago

immunooncologydatarepresentationdataimportinfrastructuresinglecell

4.16 score 73 scripts 946 downloads

moanin - An R Package for Time Course RNASeq Data Analysis

Simple and efficient workflow for time-course gene expression data, built on publictly available open-source projects hosted on CRAN and bioconductor. moanin provides helper functions for all the steps required for analysing time-course data using functional data analysis: (1) functional modeling of the timecourse data; (2) differential expression analysis; (3) clustering; (4) downstream analysis.

Last updated 2 months ago

timecoursegeneexpressionrnaseqmicroarraydifferentialexpressionclustering

4.15 score 14 scripts 397 downloads

ZygosityPredictor - Package for prediction of zygosity for variants/genes in NGS data

The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them.

Last updated 2 months ago

biomedicalinformaticsfunctionalpredictionsomaticmutationgeneprediction

4.11 score 2 scripts 120 downloads

BASiCStan - Stan implementation of BASiCS

Provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries.

Last updated 2 months ago

immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecelldifferentialexpressionbayesiancellbiologysingle-cell-rna-seqcpp

4.08 score 1 scripts 198 downloads

nearBynding - Discern RNA structure proximal to protein binding

Provides a pipeline to discern RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. CLIP protein-binding data can be input as either aligned BAM or peak-called bedGraph files. RNA structure can either be predicted internally from sequence or users have the option to input their own RNA structure data. RNA structure binding profiles can be visually and quantitatively compared across multiple formats.

Last updated 2 months ago

visualizationmotifdiscoverydatarepresentationstructuralpredictionclusteringmultiplecomparison

4.08 score 12 scripts 137 downloads

selectKSigs - Selecting the number of mutational signatures using a perplexity-based measure and cross-validation

A package to suggest the number of mutational signatures in a collection of somatic mutations using calculating the cross-validated perplexity score.

Last updated 2 months ago

softwaresomaticmutationsequencingstatisticalmethodclusteringmutational-signaturesrjagssomatic-mutationscppjags

4.08 score 3 stars 1 scripts 154 downloads

pipeFrame - Pipeline framework for bioinformatics in R

pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.

Last updated 2 months ago

softwareinfrastructureworkflowstep

4.08 score 1 stars 1 dependents 2 scripts 257 downloads

rmspc - Multiple Sample Peak Calling

The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as "peaks"), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate samples are analyzed, overlapping peaks are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. MSPC uses combined evidence from replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives. It takes any number of replicates as input and improves sensitivity and specificity of peak calling on each, and identifies consensus regions between the input samples.

Last updated 2 months ago

chipseqsequencingchiponchipdataimportrnaseqanalysischip-seqenriched-regionsgenome-analysismspcnext-generation-sequencingngs-analysisoverlapping-peakspeakpeaks

4.06 score 19 stars 5 scripts 154 downloads

PIPETS - Poisson Identification of PEaks from Term-Seq data

PIPETS provides statistically robust analysis for 3'-seq/term-seq data. It utilizes a sliding window approach to apply a Poisson Distribution test to identify genomic positions with termination read coverage that is significantly higher than the surrounding signal. PIPETS then condenses proximal signal and produces strand specific results that contain all significant termination peaks.

Last updated 2 months ago

sequencingtranscriptiongeneregulationpeakdetectiongeneticstranscriptomicscoverage

4.04 score 2 scripts 158 downloads

ClustAll - ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

Data driven strategy to find hidden groups of patients with complex diseases using clinical data. ClustAll facilitates the unsupervised identification of multiple robust stratifications. ClustAll, is able to overcome the most common limitations found when dealing with clinical data (missing values, correlated data, mixed data types).

Last updated 2 months ago

softwarestatisticalmethodclusteringdimensionreductionprincipalcomponent

4.00 score 1 scripts 184 downloads

regionalpcs - Summarizing Regional Methylation with Regional Principal Components Analysis

Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.

Last updated 2 months ago

dnamethylationdifferentialmethylationstatisticalmethodsoftwaremethylationarray

4.00 score 1 stars 4 scripts 147 downloads

plasmut - Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic

A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.

Last updated 2 months ago

bayesiansomaticmutationgermlinemutationsequencing

4.00 score 2 scripts 96 downloads

compSPOT - compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots

Clonal cell groups share common mutations within cancer, precancer, and even clinically normal appearing tissues. The frequency and location of these mutations may predict prognosis and cancer risk. It has also been well established that certain genomic regions have increased sensitivity to acquiring mutations. Mutation-sensitive genomic regions may therefore serve as markers for predicting cancer risk. This package contains multiple functions to establish significantly mutated hotspots, compare hotspot mutation burden between samples, and perform exploratory data analysis of the correlation between hotspot mutation burden and personal risk factors for cancer, such as age, gender, and history of carcinogen exposure. This package allows users to identify robust genomic markers to help establish cancer risk.

Last updated 2 months ago

softwaretechnologysequencingdnaseqwholegenomeclassificationsinglecellsurvivalmultiplecomparison

4.00 score 3 scripts 98 downloads

SARC - Statistical Analysis of Regions with CNVs

Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.

Last updated 2 months ago

softwarecopynumbervariationvisualizationdnaseqsequencing

4.00 score 2 scripts 102 downloads

orthos - `orthos` is an R package for variance decomposition using conditional variational auto-encoders

`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.

Last updated 2 months ago

rnaseqdifferentialexpressiongeneexpression

4.00 score 2 scripts 146 downloads

EDIRquery - Query the EDIR Database For Specific Gene

EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.

Last updated 2 months ago

geneticssequencematching

4.00 score 1 scripts 128 downloads

seq.hotSPOT - Targeted sequencing panel design based on mutation hotspots

seq.hotSPOT provides a resource for designing effective sequencing panels to help improve mutation capture efficacy for ultradeep sequencing projects. Using SNV datasets, this package designs custom panels for any tissue of interest and identify the genomic regions likely to contain the most mutations. Establishing efficient targeted sequencing panels can allow researchers to study mutation burden in tissues at high depth without the economic burden of whole-exome or whole-genome sequencing. This tool was developed to make high-depth sequencing panels to study low-frequency clonal mutations in clinically normal and cancerous tissues.

Last updated 2 months ago

softwaretechnologysequencingdnaseqwholegenome

4.00 score 3 scripts 108 downloads

flowGate - Interactive Cytometry Gating in R

flowGate adds an interactive Shiny app to allow manual GUI-based gating of flow cytometry data in R. Using flowGate, you can draw 1D and 2D span/rectangle gates, quadrant gates, and polygon gates on flow cytometry data by interactively drawing the gates on a plot of your data, rather than by specifying gate coordinates. This package is especially geared toward wet-lab cytometerists looking to take advantage of R for cytometry analysis, without necessarily having a lot of R experience.

Last updated 2 months ago

softwareworkflowstepflowcytometrypreprocessingimmunooncologydataimport

4.00 score 3 scripts 169 downloads

mbQTL - mbQTL: A package for SNP-Taxa mGWAS analysis

mbQTL is a statistical R package for simultaneous 16srRNA,16srDNA (microbial) and variant, SNP, SNV (host) relationship, correlation, regression studies. We apply linear, logistic and correlation based statistics to identify the relationships of taxa, genus, species and variant, SNP, SNV in the infected host. We produce various statistical significance measures such as P values, FDR, BC and probability estimation to show significance of these relationships. Further we provide various visualization function for ease and clarification of the results of these analysis. The package is compatible with dataframe, MRexperiment and text formats.

Last updated 2 months ago

snpmicrobiomewholegenomemetagenomicsstatisticalmethodregression

4.00 score 1 stars 3 scripts 121 downloads

rifiComparative - 'rifiComparative' compares the output of rifi from two different conditions.

'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

Last updated 2 months ago

rnaseqdifferentialexpressiongeneregulationtranscriptomicsmicroarraysoftware

4.00 score 135 downloads

seqArchRplus - Downstream analyses of promoter sequence architectures and HTML report generation

seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages.

Last updated 2 months ago

annotationvisualizationreportwritinggomotifannotationclustering

4.00 score 1 stars 2 scripts 151 downloads

planttfhunter - Identification and classification of plant transcription factors

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

Last updated 2 months ago

softwaretranscriptionfunctionalpredictiongenomeannotationfunctionalgenomicshiddenmarkovmodelsequencingclassificationfunctional-genomicsgene-familieshidden-markov-modelsplant-genomicsplantsprotein-domainstranscription-factors

4.00 score 5 scripts 146 downloads

MetaPhOR - Metabolic Pathway Analysis of RNA

MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.

Last updated 2 months ago

metabolomicsrnaseqpathwaysgeneexpressiondifferentialexpressionkeggsequencingmicroarray

4.00 score 1 scripts 190 downloads

magrene - Motif Analysis In Gene Regulatory Networks

magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.

Last updated 2 months ago

softwaremotifdiscoverynetworkenrichmentsystemsbiologygraphandnetworkgene-regulatory-networkmotif-analysisnetwork-motifsnetwork-science

4.00 score 1 stars 2 scripts 149 downloads

factR - Functional Annotation of Custom Transcriptomes

factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.

Last updated 2 months ago

alternativesplicingfunctionalpredictiongenepredictioncustom-transcriptomesfunctional-annotationgtfrna-seq-analysis

4.00 score 1 stars 5 scripts 132 downloads

RgnTX - Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.

Last updated 2 months ago

alternativesplicingsequencingrnaseqmethylseqtranscriptionsplicedalignment

4.00 score 6 scripts 122 downloads

SUITOR - Selecting the number of mutational signatures through cross-validation

An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data.

Last updated 2 months ago

geneticssoftwaresomaticmutation

4.00 score 2 scripts 121 downloads

biodbNcbi - biodbNcbi, a library for connecting to NCBI Databases.

The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.

Last updated 2 months ago

softwareinfrastructuredataimport

4.00 score 1 stars 1 scripts 129 downloads

biodbNci - biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database

The biodbNci library is an extension of the biodb framework package. It provides access to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database. It allows to retrieve entries by their accession number, and run specific web services.

Last updated 2 months ago

softwareinfrastructuredataimportcpp

4.00 score 2 scripts 161 downloads

xcore - xcore expression regulators inference

xcore is an R package for transcription factor activity modeling based on known molecular signatures and user's gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes.

Last updated 2 months ago

geneexpressiongeneregulationepigeneticsregressionsequencing

4.00 score 8 scripts 120 downloads

Motif2Site - Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

Last updated 2 months ago

softwaresequencingchipseqdifferentialpeakcallingepigeneticssequencematching

4.00 score 3 scripts 134 downloads

pengls - Fit Penalised Generalised Least Squares models

Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.

Last updated 2 months ago

transcriptomicsregressiontimecoursespatial

4.00 score 4 scripts 116 downloads

synapsis - An R package to automate the analysis of double-strand break repair during meiosis

Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.

Last updated 2 months ago

softwaresinglecell

4.00 score 2 scripts 120 downloads

CyTOFpower - Power analysis for CyTOF experiments

This package is a tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.

Last updated 2 months ago

flowcytometrysinglecellcellbiologystatisticalmethodsoftware

4.00 score 2 scripts 122 downloads

Cogito - Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

Last updated 2 months ago

functionalgenomicsgeneregulationsoftwaresequencing

4.00 score 3 scripts 124 downloads

pairkat - PaIRKAT

PaIRKAT is model framework for assessing statistical relationships between networks of metabolites (pathways) and an outcome of interest (phenotype). PaIRKAT queries the KEGG database to determine interactions between metabolites from which network connectivity is constructed. This model framework improves testing power on high dimensional data by including graph topography in the kernel machine regression setting. Studies on high dimensional data can struggle to include the complex relationships between variables. The semi-parametric kernel machine regression model is a powerful tool for capturing these types of relationships. They provide a framework for testing for relationships between outcomes of interest and high dimensional data such as metabolomic, genomic, or proteomic pathways. PaIRKAT uses known biological connections between high dimensional variables by representing them as edges of ‘graphs’ or ‘networks.’ It is common for nodes (e.g. metabolites) to be disconnected from all others within the graph, which leads to meaningful decreases in testing power whether or not the graph information is included. We include a graph regularization or ‘smoothing’ approach for managing this issue.

Last updated 2 months ago

softwaremetabolomicskeggpathwaysnetworkgraphandnetworkregression

4.00 score 1 scripts 176 downloads

CexoR - An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.

Last updated 2 months ago

functionalgenomicssequencingcoveragechipseqpeakdetection

4.00 score 1 scripts 248 downloads

scTreeViz - R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters.

Last updated 2 months ago

visualizationinfrastructureguisinglecell

4.00 score 3 scripts 139 downloads

surfaltr - Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.

Last updated 2 months ago

softwarevisualizationdatarepresentationsplicedalignmentalignmentmultiplesequencealignmentmultiplecomparison

4.00 score 2 scripts 131 downloads

cytoKernel - Differential expression using kernel-based score test

cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression data. In this R package, we implement functions that compute the feature-wise p values and their corresponding adjusted p values. Additionally, it also computes the feature-wise shrunk effect sizes and their corresponding shrunken effect size. Further, it calculates the percent of differentially expressed features and plots user-friendly heatmap of the top differentially expressed features on the rows and samples on the columns.

Last updated 2 months ago

immunooncologyproteomicssinglecellsoftwareonechannelflowcytometrydifferentialexpressiongeneexpressionclusteringcpp

4.00 score 4 scripts 156 downloads

metapone - Conducts pathway test of metabolomics data using a weighted permutation test

The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.

Last updated 2 months ago

technologymassspectrometrymetabolomicspathways

4.00 score 9 scripts 141 downloads

genomicInstability - Genomic Instability estimation for scRNA-Seq

This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.

Last updated 2 months ago

systemsbiologygeneexpressionsinglecell

4.00 score 5 stars 4 scripts 172 downloads

veloviz - VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories

VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.

Last updated 2 months ago

transcriptomicsvisualizationgeneexpressionsequencingrnaseqdimensionreductioncpp

4.00 score 6 scripts 132 downloads

VAExprs - Generating Samples of Gene Expression Data with Variational Autoencoders

A fundamental problem in biomedical research is the low number of observations, mostly due to a lack of available biosamples, prohibitive costs, or ethical reasons. By augmenting a few real observations with artificially generated samples, their analysis could lead to more robust and higher reproducible. One possible solution to the problem is the use of generative models, which are statistical models of data that attempt to capture the entire probability distribution from the observations. Using the variational autoencoder (VAE), a well-known deep generative model, this package is aimed to generate samples with gene expression data, especially for single-cell RNA-seq data. Furthermore, the VAE can use conditioning to produce specific cell types or subpopulations. The conditional VAE (CVAE) allows us to create targeted samples rather than completely random ones.

Last updated 2 months ago

softwaregeneexpressionsinglecellopenjdk

4.00 score 4 scripts 128 downloads

NanoTube - An Easy Pipeline for NanoString nCounter Data Analysis

NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.

Last updated 2 months ago

softwaregeneexpressiondifferentialexpressionqualitycontrol

4.00 score 7 scripts 176 downloads

systemPipeTools - Tools for data visualization

systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives.

Last updated 2 months ago

infrastructuredataimportsequencingqualitycontrolreportwritingexperimentaldesignclusteringdifferentialexpressionmultidimensionalscalingprincipalcomponent

4.00 score 4 scripts 172 downloads

POWSC - Simulation, power evaluation, and sample size recommendation for single cell RNA-seq

Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.

Last updated 2 months ago

differentialexpressionimmunooncologysinglecellsoftware

4.00 score 7 scripts 144 downloads

Rbec - Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile the microbial compositions in SynComs, but also predict the contaminants in SynCom samples.

Last updated 2 months ago

sequencingmicrobialstrainmicrobiomecpp

4.00 score 1 scripts 187 downloads

interacCircos - The Generation of Interactive Circos Plot

Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. 'interacCircos' are inspired by 'circosJS', 'BioCircos.js' and 'NG-Circos' and we integrate the modules of 'circosJS', 'BioCircos.js' and 'NG-Circos' into this R package, based on 'htmlwidgets' framework.

Last updated 2 months ago

visualization

4.00 score 1 scripts 139 downloads

mirTarRnaSeq - mirTarRnaSeq

mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.

Last updated 2 months ago

mirnaregressionsoftwaresequencingsmallrnatimecoursedifferentialexpression

4.00 score 8 scripts 152 downloads

ModCon - Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

Collection of functions to calculate a nucleotide sequence surrounding for splice donors sites to either activate or repress donor usage. The proposed alternative nucleotide sequence encodes the same amino acid and could be applied e.g. in reporter systems to silence or activate cryptic splice donor sites.

Last updated 2 months ago

functionalgenomicsalternativesplicing

4.00 score 1 stars 2 scripts 110 downloads

PhenoGeneRanker - PhenoGeneRanker: A gene and phenotype prioritization tool

This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.

Last updated 2 months ago

biomedicalinformaticsgenepredictiongraphandnetworknetworknetworkinferencepathwayssoftwaresystemsbiology

4.00 score 1 scripts 111 downloads

flowGraph - Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

Last updated 2 months ago

flowcytometrystatisticalmethodimmunooncologysoftwarecellbasedassaysvisualization

4.00 score 10 scripts 134 downloads

VarCon - VarCon: an R package for retrieving neighboring nucleotides of an SNV

VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.

Last updated 2 months ago

functionalgenomicsalternativesplicing

4.00 score 5 scripts 126 downloads

ExperimentSubset - Manages subsets of data with Bioconductor Experiment objects

Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.

Last updated 2 months ago

infrastructuresoftwaredataimportdatarepresentation

4.00 score 8 scripts 206 downloads

microbiomeExplorer - Microbiome Exploration App

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

Last updated 2 months ago

classificationclusteringgeneticvariabilitydifferentialexpressionmicrobiomemetagenomicsnormalizationvisualizationmultiplecomparisonsequencingsoftwareimmunooncology

4.00 score 8 scripts 240 downloads

tomoda - Tomo-seq data analysis

This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.

Last updated 2 months ago

geneexpressionsequencingrnaseqtranscriptomicsspatialclusteringvisualization

4.00 score 2 scripts 185 downloads

rsemmed - An interface to the Semantic MEDLINE database

A programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.

Last updated 2 months ago

softwareannotationpathwayssystemsbiology

4.00 score 8 scripts 128 downloads

hummingbird - Bayesian Hidden Markov Model for the detection of differentially methylated regions

A package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.

Last updated 2 months ago

hiddenmarkovmodelbayesiandnamethylationbiomedicalinformaticssequencinggeneexpressiondifferentialexpressiondifferentialmethylationcpp

4.00 score 1 scripts 130 downloads

Omixer - Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies

Omixer - an Bioconductor package for multivariate and reproducible sample randomization, which ensures optimal sample distribution across batches with well-documented methods. It outputs lab-friendly sample layouts, reducing the risk of sample mixups when manually pipetting randomized samples.

Last updated 2 months ago

datarepresentationexperimentaldesignqualitycontrolsoftwarevisualization

4.00 score 2 scripts 142 downloads

transomics2cytoscape - A tool set for 3D Trans-Omic network visualization with Cytoscape

transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).

Last updated 2 months ago

networksoftwarepathwaysdataimportkegg

4.00 score 2 scripts 216 downloads

GSEAmining - Make Biological Sense of Gene Set Enrichment Analysis Outputs

Gene Set Enrichment Analysis is a very powerful and interesting computational method that allows an easy correlation between differential expressed genes and biological processes. Unfortunately, although it was designed to help researchers to interpret gene expression data it can generate huge amounts of results whose biological meaning can be difficult to interpret. Many available tools rely on the hierarchically structured Gene Ontology (GO) classification to reduce reundandcy in the results. However, due to the popularity of GSEA many more gene set collections, such as those in the Molecular Signatures Database are emerging. Since these collections are not organized as those in GO, their usage for GSEA do not always give a straightforward answer or, in other words, getting all the meaninful information can be challenging with the currently available tools. For these reasons, GSEAmining was born to be an easy tool to create reproducible reports to help researchers make biological sense of GSEA outputs. Given the results of GSEA, GSEAmining clusters the different gene sets collections based on the presence of the same genes in the leadind edge (core) subset. Leading edge subsets are those genes that contribute most to the enrichment score of each collection of genes or gene sets. For this reason, gene sets that participate in similar biological processes should share genes in common and in turn cluster together. After that, GSEAmining is able to identify and represent for each cluster: - The most enriched terms in the names of gene sets (as wordclouds) - The most enriched genes in the leading edge subsets (as bar plots). In each case, positive and negative enrichments are shown in different colors so it is easy to distinguish biological processes or genes that may be of interest in that particular study.

Last updated 2 months ago

genesetenrichmentclusteringvisualization

4.00 score 7 scripts 152 downloads

GGPA - graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

Genome-wide association studies (GWAS) is a widely used tool for identification of genetic variants associated with phenotypes and diseases, though complex diseases featuring many genetic variants with small effects present difficulties for traditional these studies. By leveraging pleiotropy, the statistical power of a single GWAS can be increased. This package provides functions for fitting graph-GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy. 'GGPA' package provides user-friendly interface to fit graph-GPA models, implement association mapping, and generate a phenotype graph.

Last updated 2 months ago

softwarestatisticalmethodclassificationgenomewideassociationsnpgeneticsclusteringmultiplecomparisonpreprocessinggeneexpressiondifferentialexpressionopenblascpp

4.00 score 1 stars 2 scripts 136 downloads

receptLoss - Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors

receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the distribution of gene expression in normal tissue samples is approximated by a Gaussian. Originally designed for identifying nuclear hormone receptor expression loss but can be applied transcriptome wide as well.

Last updated 2 months ago

geneexpressionstatisticalmethod

4.00 score 2 scripts 131 downloads

frenchFISH - Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

Last updated 2 months ago

softwarebiomedicalinformaticscellbiologygeneticshiddenmarkovmodelpreprocessing

4.00 score 3 scripts 110 downloads

CSSQ - Chip-seq Signal Quantifier Pipeline

This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.

Last updated 2 months ago

chipseqdifferentialpeakcallingsequencingnormalization

4.00 score 1 scripts 148 downloads

scTGIF - Cell type annotation for unannotated single-cell RNA-Seq data

scTGIF connects the cells and the related gene functions without cell type label.

Last updated 2 months ago

dimensionreductionqualitycontrolsinglecellsoftwaregeneexpression

4.00 score 2 scripts 414 downloads

LinkHD - LinkHD: a versatile framework to explore and integrate heterogeneous data

Here we present Link-HD, an approach to integrate heterogeneous datasets, as a generalization of STATIS-ACT (“Structuration des Tableaux A Trois Indices de la Statistique–Analyse Conjointe de Tableaux”), a family of methods to join and compare information from multiple subspaces. However, STATIS-ACT has some drawbacks since it only allows continuous data and it is unable to establish relationships between samples and features. In order to tackle these constraints, we incorporate multiple distance options and a linear regression based Biplot model in order to stablish relationships between observations and variable and perform variable selection.

Last updated 2 months ago

classificationmultiplecomparisonregressionsoftware

4.00 score 2 scripts 196 downloads

ssPATHS - ssPATHS: Single Sample PATHway Score

This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set (pathway) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples.

Last updated 2 months ago

softwaregeneexpressionbiomedicalinformaticsrnaseqpathwaystranscriptomicsdimensionreductionclassification

4.00 score 1 scripts 160 downloads

GmicR - Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool.

Last updated 2 months ago

softwaresystemsbiologygraphandnetworknetworknetworkinferenceguiimmunooncologygeneexpressionqualitycontrolbayesianclustering

4.00 score 2 scripts 175 downloads

GenomicOZone - Delineate outstanding genomic zones of differential gene activity

The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.

Last updated 2 months ago

softwaregeneexpressiontranscriptiondifferentialexpressionfunctionalpredictiongeneregulationbiomedicalinformaticscellbiologyfunctionalgenomicsgeneticssystemsbiologytranscriptomicsclusteringregressionrnaseqannotationvisualizationsequencingcoveragedifferentialmethylationgenomicvariationstructuralvariationcopynumbervariation

4.00 score 203 downloads

SCANVIS - SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).

Last updated 2 months ago

softwareresearchfieldtranscriptomicsworkflowstepannotationvisualization

4.00 score 1 scripts 157 downloads

RNAmodR.ML - Detecting patterns of post-transcriptional modifications using machine learning

RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.

Last updated 2 months ago

softwareinfrastructureworkflowstepvisualizationsequencing

4.00 score 1 stars 3 scripts 158 downloads

RNAmodR.RiboMethSeq - Detection of 2'-O methylations by RiboMethSeq

RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

Last updated 2 months ago

softwareworkflowstepvisualizationsequencingbioconductormodificationsribomethseqrnarnamodr

4.00 score 1 stars 4 scripts 200 downloads

GladiaTOX - R Package for Processing High Content Screening data

GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.

Last updated 2 months ago

softwareworkflowstepnormalizationpreprocessingqualitycontrol

4.00 score 2 scripts 160 downloads

profileplyr - Visualization and annotation of read signal over genomic ranges with profileplyr

Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

Last updated 2 months ago

chipseqdataimportsequencingchiponchipcoverage

4.00 score 50 scripts 415 downloads

survtype - Subtype Identification with Survival Data

Subtypes are defined as groups of samples that have distinct molecular and clinical features. Genomic data can be analyzed for discovering patient subtypes, associated with clinical data, especially for survival information. This package is aimed to identify subtypes that are both clinically relevant and biologically meaningful.

Last updated 2 months ago

softwarestatisticalmethodgeneexpressionsurvivalclusteringsequencingcoverage

4.00 score 2 scripts 158 downloads

doseR - doseR

doseR package is a next generation sequencing package for sex chromosome dosage compensation which can be applied broadly to detect shifts in gene expression among an arbitrary number of pre-defined groups of loci. doseR is a differential gene expression package for count data, that detects directional shifts in expression for multiple, specific subsets of genes, broad utility in systems biology research. doseR has been prepared to manage the nature of the data and the desired set of inferences. doseR uses S4 classes to store count data from sequencing experiment. It contains functions to normalize and filter count data, as well as to plot and calculate statistics of count data. It contains a framework for linear modeling of count data. The package has been tested using real and simulated data.

Last updated 2 months ago

infrastructuresoftwaredatarepresentationsequencinggeneexpressionsystemsbiologydifferentialexpression

4.00 score 3 scripts 156 downloads

divergence - Divergence: Functionality for assessing omics data by divergence with respect to a baseline

This package provides functionality for performing divergence analysis as presented in Dinalankara et al, "Digitizing omics profiles by divergence from a baseline", PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features.

Last updated 2 months ago

softwarestatisticalmethod

4.00 score 10 scripts 138 downloads

adductomicsR - Processing of adductomic mass spectral datasets

Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.

Last updated 2 months ago

massspectrometrymetabolomicssoftwarethirdpartyclientdataimportgui

4.00 score 1 stars 5 scripts 340 downloads

OVESEG - OVESEG-test to detect tissue/cell-specific markers

An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes.

Last updated 2 months ago

softwaremultiplecomparisoncellbiologygeneexpressioncpp

4.00 score 1 stars 2 scripts 206 downloads

VCFArray - Representing on-disk / remote VCF files as array-like objects

VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.

Last updated 2 months ago

infrastructuredatarepresentationsequencingvariantannotation

4.00 score 1 stars 3 scripts 195 downloads

abseqR - Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.

Last updated 2 months ago

sequencingvisualizationreportwritingqualitycontrolmultiplecomparison

4.00 score 3 scripts 300 downloads

consensusDE - RNA-seq analysis using multiple algorithms

This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation.

Last updated 2 months ago

transcriptomicsmultiplecomparisonclusteringsequencingsoftware

4.00 score 10 scripts 170 downloads

HIREewas - Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.

Last updated 2 months ago

dnamethylationdifferentialmethylationfeatureextraction

4.00 score 1 scripts 165 downloads

KinSwingR - KinSwingR: network-based kinase activity prediction

KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity.

Last updated 2 months ago

proteomicssequencematchingnetwork

4.00 score 4 scripts 156 downloads

Rcollectl - Help use collectl with R in Linux, to measure resource consumption in R processes

Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.

Last updated 2 months ago

softwareinfrastructure

3.95 score 3 stars 7 scripts 70 downloads

BOBaFIT - Refitting diploid region profiles using a clustering procedure

This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.

Last updated 2 months ago

copynumbervariationclusteringvisualizationnormalizationsoftware

3.90 score 3 scripts 167 downloads

CGEN - An R package for analysis of case-control studies in genetic epidemiology

This is a package for analysis of case-control data in genetic epidemiology. It provides a set of statistical methods for evaluating gene-environment (or gene-genes) interactions under multiplicative and additive risk models, with or without assuming gene-environment (or gene-gene) independence in the underlying population.

Last updated 2 months ago

snpmultiplecomparisonclusteringfortran

3.90 score 10 scripts 220 downloads

GWAS.BAYES - Bayesian analysis of Gaussian GWAS data

This package is built to perform GWAS analysis using Bayesian techniques. Currently, GWAS.BAYES has functionality for the implementation of BICOSS (Williams, J., Ferreira, M. A., and Ji, T. (2022). BICOSS: Bayesian iterative conditional stochastic search for GWAS. BMC Bioinformatics), BGWAS (Williams, J., Xu, S., Ferreira, M. A.. (2023) "BGWAS: Bayesian variable selection in linear mixed models with nonlocal priors for genome-wide association studies." BMC Bioinformatics), and GINA. All methods currently are for the analysis of Gaussian phenotypes The research related to this package was supported in part by National Science Foundation awards DMS 1853549, DMS 1853556, and DMS 2054173.

Last updated 2 months ago

bayesianassaydomainsnpgenomewideassociation

3.90 score 8 scripts 200 downloads

getDEE2 - Programmatic access to the DEE2 RNA expression dataset

Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).

Last updated 2 months ago

geneexpressiontranscriptomicssequencingbioinformaticsdata-mininggenomicsrna-expressionrna-seq

3.90 score 4 stars 5 scripts 132 downloads

flowCut - Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis

Common techinical complications such as clogging can result in spurious events and fluorescence intensity shifting, flowCut is designed to detect and remove technical artifacts from your data by removing segments that show statistical differences from other segments.

Last updated 2 months ago

flowcytometrypreprocessingqualitycontrolcellbasedassays

3.90 score 20 scripts 225 downloads

scTHI - Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data

scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment.

Last updated 2 months ago

softwaresinglecell

3.90 score 4 stars 2 scripts 130 downloads

DMCFB - Differentially Methylated Cytosines via a Bayesian Functional Approach

DMCFB is a pipeline for identifying differentially methylated cytosines using a Bayesian functional regression model in bisulfite sequencing data. By using a functional regression data model, it tries to capture position-specific, group-specific and other covariates-specific methylation patterns as well as spatial correlation patterns and unknown underlying models of methylation data. It is robust and flexible with respect to the true underlying models and inclusion of any covariates, and the missing values are imputed using spatial correlation between positions and samples. A Bayesian approach is adopted for estimation and inference in the proposed method.

Last updated 2 months ago

differentialmethylationsequencingcoveragebayesianregression

3.90 score 3 scripts 191 downloads

cypress - Cell-Type-Specific Power Assessment

CYPRESS is a cell-type-specific power tool. This package aims to perform power analysis for the cell-type-specific data. It calculates FDR, FDC, and power, under various study design parameters, including but not limited to sample size, and effect size. It takes the input of a SummarizeExperimental(SE) object with observed mixture data (feature by sample matrix), and the cell-type mixture proportions (sample by cell-type matrix). It can solve the cell-type mixture proportions from the reference free panel from TOAST and conduct tests to identify cell-type-specific differential expression (csDE) genes.

Last updated 2 months ago

softwaregeneexpressiondataimportrnaseqsequencing

3.88 score 1 stars 2 scripts 144 downloads

srnadiff - Finding differentially expressed unannotated genomic regions from RNA-seq data

srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.

Last updated 4 days ago

immunooncologygeneexpressioncoveragesmallrnaepigeneticsstatisticalmethodpreprocessingdifferentialexpressioncpp

3.85 score 3 scripts 208 downloads

Rfastp - An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.

Last updated 2 months ago

qualitycontrolsequencingpreprocessingsoftwarezlibcpp

3.82 score 33 scripts 301 downloads

RegEnrich - Gene regulator enrichment analysis

This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.

Last updated 2 months ago

geneexpressiontranscriptomicsrnaseqtwochanneltranscriptiongenetargetnetworkenrichmentdifferentialexpressionnetworknetworkinferencegenesetenrichmentfunctionalprediction

3.82 score 22 scripts 198 downloads

BiocHubsShiny - View AnnotationHub and ExperimentHub Resources Interactively

A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.

Last updated 3 days ago

softwareshinyapps

3.78 score 1 scripts 148 downloads

netDx - Network-based patient classifier

netDx is a general-purpose algorithm to build a patient classifier from heterogenous patient data. The method converts data into patient similarity networks at the level of features. Feature selection identifies features of predictive value to each class. Methods are provided for versatile predictor design and performance evaluation using standard measures. netDx natively groups molecular data into pathway-level features and connects with Cytoscape for network visualization of pathway themes. For method details see: Pai et al. (2019). netDx: interpretable patient classification using integrated patient similarity networks. Molecular Systems Biology. 15, e8497

Last updated 5 days ago

classificationbiomedicalinformaticsnetworksystemsbiology

3.78 score 2 scripts 116 downloads

pfamAnalyzeR - Identification of domain isotypes in pfam data

Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data.

Last updated 2 months ago

alternativesplicingtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologyannotationfunctionalpredictiongenepredictiondataimport

3.78 score 1 stars 1 dependents 1 scripts 450 downloads

flowVS - Variance stabilization in flow cytometry (and microarrays)

Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.

Last updated 2 months ago

immunooncologyflowcytometrycellbasedassaysmicroarray

3.78 score 10 scripts 292 downloads

CONSTANd - Data normalization by matrix raking

Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the row means and column means equal 1. The result is a normalized data matrix `K=RAS`, a product of row mulipliers `R` and column multipliers `S` with the original matrix `A`. Missing information needs to be presented as `NA` values and not as zero values, because CONSTANd is able to ignore missing values when calculating the mean. Using CONSTANd normalization allows for the direct comparison of values between samples within the same and even across different CONSTANd-normalized data matrices.

Last updated 2 months ago

massspectrometrycheminformaticsnormalizationpreprocessingdifferentialexpressiongeneticstranscriptomicsproteomics

3.78 score 3 scripts 125 downloads

famat - Functional analysis of metabolic and transcriptomic data

Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user's genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user's elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user's genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.

Last updated 2 months ago

functionalpredictiongenesetenrichmentpathwaysgoreactomekeggcompoundgene-ontologygenesshiny

3.78 score 1 stars 2 scripts 157 downloads

infinityFlow - Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions

Pipeline to analyze and merge data files produced by BioLegend's LEGENDScreen or BD Human Cell Surface Marker Screening Panel (BD Lyoplates).

Last updated 2 months ago

softwareflowcytometrycellbasedassayssinglecellproteomics

3.78 score 4 scripts 210 downloads

SubCellBarCode - SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.

Last updated 2 months ago

proteomicsmassspectrometryclassification

3.78 score 1 scripts 159 downloads

MPAC - Multi-omic Pathway Analysis of Cancer

Multi-omic Pathway Analysis of Cancer (MPAC), integrates multi-omic data for understanding cancer mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.

Last updated 2 months ago

softwaretechnologysequencingrnaseqsurvivalclusteringimmunooncology

3.74 score 1 scripts 86 downloads

supraHex - supraHex: a supra-hexagonal map for analysing tabular omics data

A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics input data. The supraHex is able to carry out gene clustering/meta-clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. So with supraHex, it is also possible to carry out multilayer omics data comparisons. Newly added utilities are advanced heatmap visualisation and tree-based analysis of sample relationships. Uniquely to this package, users can ultrafastly understand any tabular omics data, both scientifically and artistically, especially in a sample-specific fashion but without loss of information on large genes.

Last updated 5 days ago

softwareclusteringvisualizationgeneexpression

3.73 score 20 scripts 746 downloads

borealis - Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detectes outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses.

Last updated 2 months ago

sequencingcoveragednamethylationdifferentialmethylation

3.73 score 27 scripts 147 downloads

LimROTS - A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics and Metabolomics Data

Differential expression analysis is a prevalent method utilised in the examination of diverse biological data. The reproducibility-optimized test statistic (ROTS) modifies a t-statistic based on the data's intrinsic characteristics and ranks features according to their statistical significance for differential expression between two or more groups (f-statistic). Focussing on proteomics and metabolomics, the current ROTS implementation cannot account for technical or biological covariates such as MS batches or gender differences among the samples. Consequently, we developed LimROTS, which employs a reproducibility-optimized test statistic utilising the limma methodology to simulate complex experimental designs. LimROTS is a hybrid method integrating empirical bayes and reproducibility-optimized statistics for robust analysis of proteomics and metabolomics data.

Last updated 2 days ago

softwaregeneexpressiondifferentialexpressionmicroarrayrnaseqproteomicsimmunooncologymetabolomicsmrnamicroarray

3.70 score 1 stars 1 scripts

PRONE - The PROteomics Normalization Evaluator

High-throughput omics data are often affected by systematic biases introduced throughout all the steps of a clinical study, from sample collection to quantification. Normalization methods aim to adjust for these biases to make the actual biological signal more prominent. However, selecting an appropriate normalization method is challenging due to the wide range of available approaches. Therefore, a comparative evaluation of unnormalized and normalized data is essential in identifying an appropriate normalization strategy for a specific data set. This R package provides different functions for preprocessing, normalizing, and evaluating different normalization approaches. Furthermore, normalization methods can be evaluated on downstream steps, such as differential expression analysis and statistical enrichment analysis. Spike-in data sets with known ground truth and real-world data sets of biological experiments acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can be analyzed.

Last updated 2 months ago

proteomicspreprocessingnormalizationdifferentialexpressionvisualizationdata-analysisevaluation

3.70 score 1 stars 7 scripts

MsBackendMetaboLights - Retrieve Mass Spectrometry Data from MetaboLights

MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

Last updated 2 months ago

infrastructuremassspectrometrymetabolomicsdataimportproteomicsmass-spectrometrymetabolomics-data

3.70 score 2 stars 7 scripts

omada - Machine learning tools for automated transcriptome clustering analysis

Symptomatic heterogeneity in complex diseases reveals differences in molecular states that need to be investigated. However, selecting the numerous parameters of an exploratory clustering analysis in RNA profiling studies requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent and further gene association analyses need to be performed independently. We have developed a suite of tools to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions. The efficiency of each tool was tested with four datasets characterised by different expression signal strengths. Our toolkit’s decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Even in datasets with less clear biological distinctions, stable subgroups with different expression profiles and clinical associations were found.

Last updated 2 months ago

softwareclusteringrnaseqgeneexpression

3.70 score 5 scripts 106 downloads

rebook - Re-using Content in Bioconductor Books

Provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment.

Last updated 2 months ago

softwareinfrastructurereportwriting

3.64 score 220 scripts 220 downloads

HTSeqGenie - A NGS analysis pipeline.

Libraries to perform NGS analysis.

Last updated 5 days ago

3.60 score 4 scripts 176 downloads

kmcut - Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers

The purpose of the package is to identify prognostic biomarkers and an optimal numeric cutoff for each biomarker that can be used to stratify a group of test subjects (samples) into two sub-groups with significantly different survival (better vs. worse). The package was developed for the analysis of gene expression data, such as RNA-seq. However, it can be used with any quantitative variable that has a sufficiently large proportion of unique values.

Last updated 2 months ago

softwarestatisticalmethodgeneexpressionsurvival

3.60 score 1 scripts 111 downloads

randRotation - Random Rotation Methods for High Dimensional Data with Batch Structure

A collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods.

Last updated 2 months ago

softwaresequencingbatcheffectbiomedicalinformaticsrnaseqpreprocessingmicroarraydifferentialexpressiongeneexpressiongeneticsmicrornaarraynormalizationstatisticalmethod

3.60 score 3 scripts 118 downloads

rfaRm - An R interface to the Rfam database

rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

Last updated 2 months ago

functionalgenomicsdataimportthirdpartyclientvisualizationmultiplesequencealignment

3.60 score 1 scripts 154 downloads

ssrch - a simple search engine

Demonstrate tokenization and a search gadget for collections of CSV files.

Last updated 2 months ago

infrastructure

3.60 score 20 scripts 114 downloads

interactiveDisplay - Package for enabling powerful shiny web displays of Bioconductor objects

The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.

Last updated 4 days ago

gogeneexpressionmicroarraysequencingclassificationnetworkqualitycontrolvisualizationgeneticsdatarepresentationguiannotationdatashinyapps

3.48 score 4 scripts 470 downloads

Biostrings - Efficient manipulation of biological strings

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Last updated 8 days ago

sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package

17.85 score 58 stars 1.2k dependents 8.6k scripts 99k downloads

rhdf5 - R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Last updated 13 days ago

infrastructuredataimporthdf5rhdf5opensslcurlzlibcpp

16.10 score 61 stars 234 dependents 4.2k scripts 35k downloads

enrichplot - Visualization of Functional Enrichment Result

The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualization methods are developed based on 'ggplot2' graphics.

Last updated 8 days ago

annotationgenesetenrichmentgokeggpathwayssoftwarevisualizationenrichment-analysispathway-analysis

15.72 score 237 stars 60 dependents 3.2k scripts 31k downloads

GSVA - Gene Set Variation Analysis for Microarray and RNA-Seq Data

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

Last updated 5 days ago

functionalgenomicsmicroarrayrnaseqpathwaysgenesetenrichmentgene-set-enrichmentgenomicspathway-enrichment-analysis

14.71 score 205 stars 19 dependents 1.6k scripts 12k downloads

xcms - LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Last updated 7 days ago

immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp

14.36 score 189 stars 11 dependents 928 scripts 3.3k downloads

iSEE - Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Last updated 12 days ago

cellbasedassaysclusteringdimensionreductionfeatureextractiongeneexpressionguiimmunooncologyshinyappssinglecelltranscriptiontranscriptomicsvisualizationdimension-reductionfeature-extractiongene-expressionhacktoberfesthuman-cell-atlasshinysingle-cell

12.80 score 224 stars 9 dependents 364 scripts 832 downloads

bsseq - Analyze, manage and store whole-genome methylation data

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Last updated 6 days ago

dnamethylationcpp

12.28 score 36 stars 16 dependents 664 scripts 2.5k downloads

glmGamPoi - Fit a Gamma-Poisson Generalized Linear Model

Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.

Last updated 12 days ago

regressionrnaseqsoftwaresinglecellgamma-poissonglmnegative-binomial-regressionon-diskopenblascpp

12.05 score 105 stars 4 dependents 924 scripts 8.7k downloads

beachmat - Compiling Bioconductor to Handle Each Matrix Type

Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.

Last updated 7 days ago

datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-librarycpp

11.06 score 4 stars 136 dependents 21 scripts 30k downloads

ORFik - Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Last updated 9 days ago

immunooncologysoftwaresequencingriboseqrnaseqfunctionalgenomicscoveragealignmentdataimportcpp

10.60 score 33 stars 2 dependents 116 scripts 364 downloads

BiocNeighbors - Nearest Neighbor Detection for Bioconductor Packages

Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.

Last updated 12 days ago

clusteringclassificationcpp

10.12 score 85 dependents 618 scripts 19k downloads

derfinder - Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

Last updated 9 days ago

differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder

10.03 score 42 stars 6 dependents 78 scripts 962 downloads

DropletUtils - Utilities for Handling Single-Cell Droplet Data

Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.

Last updated 11 days ago

immunooncologysinglecellsequencingrnaseqgeneexpressiontranscriptomicsdataimportcoveragezlibcpp

9.98 score 8 dependents 2.4k scripts 4.1k downloads

recount - Explore and download data from the recount project

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Last updated 9 days ago

coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount

9.56 score 40 stars 3 dependents 502 scripts 630 downloads

matter - Out-of-core statistical computing and signal processing

Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.

Last updated 17 days ago

infrastructuredatarepresentationdataimportdimensionreductionpreprocessingcpp

9.55 score 57 stars 2 dependents 65 scripts 466 downloads

TCGAutils - TCGA utility functions for data management

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

Last updated 5 days ago

softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgautilities

9.54 score 23 stars 8 dependents 203 scripts 1.3k downloads

Rsubread - Mapping, quantification and variant analysis of sequencing data

Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

Last updated 6 days ago

sequencingalignmentsequencematchingrnaseqchipseqsinglecellgeneexpressiongeneregulationgeneticsimmunooncologysnpgeneticvariabilitypreprocessingqualitycontrolgenomeannotationgenefusiondetectionindeldetectionvariantannotationvariantdetectionmultiplesequencealignmentzlib

9.05 score 10 dependents 860 scripts 3.6k downloads

scPipe - Pipeline for single cell multi-omic data pre-processing

A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.

Last updated 5 days ago

immunooncologysoftwaresequencingrnaseqgeneexpressionsinglecellvisualizationsequencematchingpreprocessingqualitycontrolgenomeannotationdataimportcurlbzip2xz-utilszlibcpp

9.02 score 69 stars 84 scripts 330 downloads

Rdisop - Decomposition of Isotopic Patterns

In high resolution mass spectrometry (HR-MS), the measured masses can be decomposed into potential element combinations (chemical sum formulas). Where additional mass/intensity information of respective isotopic peaks is available, decomposition can take this information into account to better rank the potential candidate sum formulas. To compare measured mass/intensity information with the theoretical distribution of candidate sum formulas, the latter needs to be calculated. This package implements fast algorithms to address both tasks, the calculation of isotopic distributions for arbitrary sum formulas (assuming a HR-MS resolution of roughly 30,000), and the ranked list of sum formulas fitting an observed peak or isotopic peak set.

Last updated 12 days ago

immunooncologymassspectrometrymetabolomicscpp

9.00 score 4 stars 2 dependents 100 scripts 1.2k downloads

lefser - R implementation of the LEfSE method for microbiome biomarker discovery

lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).

Last updated 5 days ago

softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-package

8.89 score 51 stars 1 dependents 58 scripts 913 downloads

affyio - Tools for parsing Affymetrix data files

Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.

Last updated 7 days ago

microarraydataimportinfrastructurezlib

8.85 score 3 stars 115 dependents 42 scripts 12k downloads

trackViewer - A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

Last updated 13 days ago

visualization

8.83 score 2 dependents 146 scripts 1.2k downloads

AnVIL - Bioconductor on the AnVIL compute environment

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

Last updated 5 days ago

infrastructure

8.70 score 10 dependents 229 scripts 1.0k downloads

CompoundDb - Creating and Using (Chemical) Compound Annotation Databases

CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

Last updated 8 days ago

massspectrometrymetabolomicsannotationdatabasesmass-spectrometry

8.38 score 17 stars 1 dependents 66 scripts 480 downloads

ClassifyR - A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

The software formalises a framework for classification and survival model evaluation in R. There are four stages; Data transformation, feature selection, model training, and prediction. The requirements of variable types and variable order are fixed, but specialised variables for functions can also be provided. The framework is wrapped in a driver loop that reproducibly carries out a number of cross-validation schemes. Functions for differential mean, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.

Last updated 16 days ago

classificationsurvivalcpp

8.22 score 5 stars 3 dependents 44 scripts 574 downloads

pwalign - Perform pairwise sequence alignments

The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

Last updated 15 days ago

alignmentsequencematchingsequencinggeneticsbioconductor-package

8.22 score 1 stars 106 dependents 23 scripts 7.5k downloads

csaw - ChIP-Seq Analysis with Windows

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Last updated 5 days ago

multiplecomparisonchipseqnormalizationsequencingcoveragegeneticsannotationdifferentialpeakcallingcurlbzip2xz-utilszlibcpp

8.19 score 7 dependents 490 scripts 893 downloads

recount3 - Explore and download data from the recount3 project

The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.

Last updated 11 days ago

coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3

7.91 score 31 stars 174 scripts 455 downloads

biocthis - Automate package and project setup for Bioconductor packages

This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.

Last updated 11 days ago

softwarereportwritingactionsbioconductorbiocthisgithubstylerusethis

7.77 score 50 stars 1 dependents 4 scripts 509 downloads

topconfects - Top Confident Effect Sizes

Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors.

Last updated 12 days ago

geneexpressiondifferentialexpressiontranscriptomicsrnaseqmrnamicroarrayregressionmultiplecomparison

7.38 score 14 stars 2 dependents 18 scripts 292 downloads

gDRimport - Package for handling the import of dose-response data

The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.

Last updated 12 days ago

softwareinfrastructuredataimport

7.11 score 2 stars 1 dependents 5 scripts 142 downloads

gDRutils - A package with helper functions for processing drug response data

This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.

Last updated 5 days ago

softwareinfrastructure

7.10 score 3 dependents 3 scripts 146 downloads

regionReport - Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.

Last updated 9 days ago

differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown

7.07 score 9 stars 44 scripts 314 downloads

NanoMethViz - Visualise methylation data from Oxford Nanopore sequencing

NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.

Last updated 2 months ago

softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimportzlibcpp

6.98 score 24 stars 12 scripts 260 downloads

affyPLM - Methods for fitting probe-level models

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

Last updated 7 days ago

microarrayonechannelpreprocessingqualitycontrolopenblaszlib

6.76 score 4 dependents 204 scripts 1.6k downloads

SRAdb - A compilation of metadata from NCBI SRA and tools

The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

Last updated 11 days ago

infrastructuresequencingdataimport

6.51 score 2 stars 200 scripts 741 downloads

MSstatsConvert - Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages.

Last updated 9 days ago

massspectrometryproteomicssoftwaredataimportqualitycontrol

6.37 score 7 dependents 25 scripts 639 downloads

derfinderHelper - derfinder helper package

Helper package for speeding up the derfinder package when using multiple cores. This package is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.

Last updated 9 days ago

differentialexpressionsequencingrnaseqsoftwareimmunooncologybioconductorderfinder

6.20 score 7 dependents 864 downloads

megadepth - megadepth: BigWig and BAM related utilities

This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.

Last updated 9 days ago

softwarecoveragedataimporttranscriptomicsrnaseqpreprocessingbambigwigdasptermegadepthrecount2recount3

6.17 score 11 stars 1 dependents 7 scripts 372 downloads

HiCDOC - A/B compartment detection and differential analysis

HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.

Last updated 10 days ago

hicdna3dstructurenormalizationsequencingsoftwareclusteringcpp

5.98 score 4 stars 1 dependents 6 scripts 202 downloads

seqsetvis - Set Based Visualizations for Next-Gen Sequencing Data

seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

Last updated 12 days ago

softwarechipseqmultiplecomparisonsequencingvisualization

5.97 score 77 scripts 260 downloads

BioNAR - Biological Network Analysis in R

the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

Last updated 11 days ago

softwaregraphandnetworknetwork

5.87 score 3 stars 35 scripts 187 downloads

CellBarcode - Cellular DNA Barcode Analysis toolkit

The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.

Last updated 6 days ago

preprocessingqualitycontrolsequencingcrisprampliconamplicon-sequencingcellular-barcodecpp

5.78 score 1 stars 40 scripts 149 downloads

ISAnalytics - Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

In gene therapy, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites (IS), essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at (1) supporting automation of IS workflow, (2) performing base and advance analysis for IS tracking (clonal abundance, clonal expansions and statistics for insertional mutagenesis, etc.), (3) providing basic biology insights of transduced stem cells in vivo.

Last updated 17 days ago

biomedicalinformaticssequencingsinglecell

5.73 score 3 stars 15 scripts 153 downloads

diffHic - Differential Analysis of Hi-C Data

Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.

Last updated 5 days ago

multiplecomparisonpreprocessingsequencingcoveragealignmentnormalizationclusteringhiccurlbzip2xz-utilszlibcpp

5.58 score 38 scripts 288 downloads

DegCre - Probabilistic association of DEGs to CREs from differential data

DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats.

Last updated 8 days ago

geneexpressiongeneregulationatacseqchipseqdnaseseqrnaseq

5.54 score 5 stars 2 scripts 132 downloads

scifer - Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Have you ever index sorted cells in a 96 or 384-well plate and then sequenced using Sanger sequencing? If so, you probably had some struggles to either check the electropherogram of each cell sequenced manually, or when you tried to identify which cell was sorted where after sequencing the plate. Scifer was developed to solve this issue by performing basic quality control of Sanger sequences and merging flow cytometry data from probed single-cell sorted B cells with sequencing data. scifer can export summary tables, 'fasta' files, electropherograms for visual inspection, and generate reports.

Last updated 9 days ago

preprocessingqualitycontrolsangerseqsequencingsoftwareflowcytometrysinglecell

5.54 score 5 stars 10 scripts 140 downloads

CytoMDS - Low Dimensions projection of cytometry samples

This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.

Last updated 13 days ago

flowcytometryqualitycontroldimensionreductionmultidimensionalscalingsoftwarevisualization

5.43 score 1 stars 2 scripts 132 downloads

qsvaR - Generate Quality Surrogate Variable Analysis for Degradation Correction

The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.

Last updated 11 days ago

softwareworkflowstepnormalizationbiologicalquestiondifferentialexpressionsequencingcoveragebioconductorbraindegradationhumanqsva

5.43 score 4 scripts 372 downloads

visiumStitched - Enable downstream analysis of Visium capture areas stitched together with Fiji

This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexogonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.

Last updated 8 days ago

softwarespatialtranscriptomicstranscriptiongeneexpressionvisualizationdataimport10xgenomicsbioconductorspatial-transcriptomicsspatialexperimentspatiallibdvisium

5.40 score 1 stars 4 scripts

hoodscanR - Spatial cellular neighbourhood scanning in R

hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.

Last updated 17 days ago

spatialtranscriptomicssinglecellclusteringcpp

5.26 score 4 stars 13 scripts 122 downloads

regutools - regutools: an R package for data extraction from RegulonDB

RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.

Last updated 11 days ago

generegulationgeneexpressionsystemsbiologynetworknetworkinferencevisualizationtranscriptionbioconductorcdsbregulondb

5.20 score 4 stars 6 scripts 198 downloads

TREG - Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.

Last updated 11 days ago

softwaresinglecellrnaseqgeneexpressiontranscriptomicstranscriptionsequencingbioconductordeconvolutionrnascopescrna-seqsmfishsnrna-seqtreg

5.20 score 4 stars 5 scripts 145 downloads

derfinderPlot - Plotting functions for derfinder

This package provides plotting functions for results from the derfinder package. This helps separate the graphical dependencies required for making these plots from the core functionality of derfinder.

Last updated 9 days ago

differentialexpressionsequencingrnaseqsoftwarevisualizationimmunooncologybioconductorderfinder

5.00 score 2 stars 5 scripts 279 downloads

scMitoMut - Single-cell Mitochondrial Mutation Analysis Tool

This package is designed for calling lineage-informative mitochondrial mutations using single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the latter due to RNA editing issues). It includes functions for mutation calling and visualization. Mutation calling is done using beta-binomial distribution.

Last updated 6 days ago

preprocessingsequencingsinglecellopenblascpp

4.95 score 2 stars 4 scripts 130 downloads

SurfR - Surface Protein Prediction and Identification

Identify Surface Protein coding genes from a list of candidates. Systematically download data from GEO and TCGA or use your own data. Perform DGE on bulk RNAseq data. Perform Meta-analysis. Descriptive enrichment analysis and plots.

Last updated 8 days ago

softwaresequencingrnaseqgeneexpressiontranscriptiondifferentialexpressionprincipalcomponentgenesetenrichmentpathwaysbatcheffectfunctionalgenomicsvisualizationdataimportfunctionalpredictiongenepredictiongodgeenrichment-analysismetaanalysisplotsproteinspublic-datasurfacesurfaceome

4.90 score 1 stars 3 scripts 120 downloads

VisiumIO - Import Visium data from the 10X Space Ranger pipeline

The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.

Last updated 16 days ago

softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomics

4.89 score 11 scripts 104 downloads

screenCounter - Counting Reads in High-Throughput Sequencing Screens

Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data.

Last updated 10 days ago

crispralignmentfunctionalgenomicsfunctionalpredictionzlibcpp

4.78 score 3 stars 10 scripts 138 downloads

BufferedMatrix - A matrix data storage object held in temporary files

A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.

Last updated 7 days ago

infrastructure

4.73 score 1 dependents 6 scripts 320 downloads

GrafGen - Classification of Helicobacter Pylori Genomes

To classify Helicobacter pylori genomes according to genetic distance from nine reference populations. The nine reference populations are hpgpAfrica, hpgpAfrica-distant, hpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope, hpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex populations are Africa, Europe and Asia.

Last updated 5 days ago

geneticssoftwaregenomeannotationclassificationcpp

4.65 score 2 scripts 132 downloads

quantiseqr - Quantification of the Tumor Immune contexture from RNA-seq data

This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data.

Last updated 5 days ago

geneexpressionsoftwaretranscriptiontranscriptomicssequencingmicroarrayvisualizationannotationimmunooncologyfeatureextractionclassificationstatisticalmethodexperimenthubsoftwareflowcytometry

4.65 score 1 dependents 2 scripts 794 downloads

G4SNVHunter - Evaluating SNV-Induced Disruption of G-Quadruplex Structures

G-quadruplexes (G4s) are unique nucleic acid secondary structures predominantly found in guanine-rich regions and have been shown to be involved in various biological regulatory processes. G4SNVHunter is an R package designed to rapidly identify genomic sequences with G4-forming potential and accurately screen user-provided single nucleotide variants (also applicable to single nucleotide polymorphisms) that may destabilize these structures. This enables users to screen key variants for further experimental study, investigating how these variants may influence biological functions, such as gene regulation, by altering G4 formation.

Last updated 10 days ago

epigeneticssnpcpp

4.48 score 4 scripts

REBET - The subREgion-based BurdEn Test (REBET)

There is an increasing focus to investigate the association between rare variants and diseases. The REBET package implements the subREgion-based BurdEn Test which is a powerful burden test that simultaneously identifies susceptibility loci and sub-regions.

Last updated 9 days ago

softwarevariantannotationsnp

4.30 score 2 scripts 185 downloads

RegionalST - Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

Last updated 16 days ago

spatialtranscriptomicsreactomekegg

4.30 score 8 scripts 130 downloads

RiboDiPA - Differential pattern analysis for Ribo-seq data

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

Last updated 16 days ago

riboseqgeneexpressiongeneregulationdifferentialexpressionsequencingcoveragealignmentrnaseqimmunooncologyqualitycontroldataimportsoftwarenormalizationcpp

4.30 score 1 scripts 147 downloads

SOMNiBUS - Smooth modeling of bisulfite sequencing

This package aims to analyse count-based methylation data on predefined genomic regions, such as those obtained by targeted sequencing, and thus to identify differentially methylated regions (DMRs) that are associated with phenotypes or traits. The method is built a rich flexible model that allows for the effects, on the methylation levels, of multiple covariates to vary smoothly along genomic regions. At the same time, this method also allows for sequencing errors and can adjust for variability in cell type mixture.

Last updated 8 months ago

dnamethylationregressionepigeneticsdifferentialmethylationsequencingfunctionalprediction

4.00 score 1 stars 3 scripts 128 downloads

chopsticks - The 'snp.matrix' and 'X.snp.matrix' Classes

Implements classes and methods for large-scale SNP association studies

Last updated 17 days ago

microarraysnpsandgeneticvariabilitysnpgeneticvariability

3.48 score 5 scripts 251 downloads

biomvRCNS - Copy Number study and Segmentation for multivariate biological data

In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.

Last updated 2 months ago

acghcopynumbervariationmicroarraysequencingvisualizationgenetics

3.48 score 2 scripts 334 downloads

TRESS - Toolbox for mRNA epigenetics sequencing analysis

This package is devoted to analyzing MeRIP-seq data. Current functionalities include 1. detect transcriptome wide m6A methylation regions 2. detect transcriptome wide differential m6A methylation regions.

Last updated 2 months ago

epigeneticsrnaseqpeakdetectiondifferentialmethylation

3.48 score 1 dependents 5 scripts 173 downloads

deltaCaptureC - This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.

Last updated 2 months ago

biologicalquestionstatisticalmethod

3.48 score 1 scripts 170 downloads

methodical - Discovering genomic regions where methylation is strongly associated with transcriptional activity

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

Last updated 2 months ago

dnamethylationmethylationarraytranscriptiongenomewideassociationsoftware

3.41 score 15 scripts 116 downloads

DeProViR - A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Protein-Protein Interactions

Emerging infectious diseases, exemplified by the zoonotic COVID-19 pandemic caused by SARS-CoV-2, are grave global threats. Understanding protein-protein interactions (PPIs) between host and viral proteins is essential for therapeutic targets and insights into pathogen replication and immune evasion. While experimental methods like yeast two-hybrid screening and mass spectrometry provide valuable insights, they are hindered by experimental noise and costs, yielding incomplete interaction maps. Computational models, notably DeProViR, predict PPIs from amino acid sequences, incorporating semantic information with GloVe embeddings. DeProViR employs a Siamese neural network, integrating convolutional and Bi-LSTM networks to enhance accuracy. It overcomes the limitations of feature engineering, offering an efficient means to predict host-virus interactions, which holds promise for antiviral therapies and advancing our understanding of infectious diseases.

Last updated 2 months ago

proteomicssystemsbiologynetworkinferenceneuralnetworknetwork

3.40 score 1 stars 1 scripts 140 downloads

ncRNAtools - An R toolkit for non-coding RNA

ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures.

Last updated 2 months ago

functionalgenomicsdataimportthirdpartyclientvisualizationstructuralprediction

3.38 score 1 stars 12 scripts 154 downloads

ProteoMM - Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).

Last updated 2 months ago

immunooncologymassspectrometryproteomicsnormalizationdifferentialexpression

3.38 score 12 scripts 206 downloads

RGMQL - GenoMetric Query Language for R/Bioconductor

This package brings the GenoMetric Query Language (GMQL) functionalities into the R environment. GMQL is a high-level, declarative language to manage heterogeneous genomic datasets for biomedical purposes, using simple queries to process genomic regions and their metadata and properties. GMQL adopts algorithms efficiently designed for big data using cloud-computing technologies (like Apache Hadoop and Spark) allowing GMQL to run on modern infrastructures, in order to achieve scalability and high performance. It allows to create, manipulate and extract genomic data from different data sources both locally and remotely. Our RGMQL functions allow complex queries and processing leveraging on the R idiomatic paradigm. The RGMQL package also provides a rich set of ancillary classes that allow sophisticated input/output management and sorting, such as: ASC, DESC, BAG, MIN, MAX, SUM, AVG, MEDIAN, STD, Q1, Q2, Q3 (and many others). Note that many RGMQL functions are not directly executed in R environment, but are deferred until real execution is issued.

Last updated 5 days ago

softwareinfrastructuredataimportnetworkimmunooncologysinglecellopenjdk

3.30 score 7 scripts 148 downloads

rGenomeTracks - Integerated visualization of epigenomic data

rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.

Last updated 2 months ago

softwarehicvisualization

3.30 score 2 scripts 162 downloads

NeuCA - NEUral network-based single-Cell Annotation tool

NeuCA is is a neural-network based method for scRNA-seq data annotation. It can automatically adjust its classification strategy depending on cell type correlations, to accurately annotate cell. NeuCA can automatically utilize the structure information of the cell types through a hierarchical tree to improve the annotation accuracy. It is especially helpful when the data contain closely correlated cell types.

Last updated 2 months ago

singlecellsoftwareclassificationneuralnetworkrnaseqtranscriptomicsdatarepresentationtranscriptionsequencingpreprocessinggeneexpressiondataimport

3.30 score 3 scripts 102 downloads

DExMA - Differential Expression Meta-Analysis

performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.

Last updated 2 months ago

differentialexpressiongeneexpressionstatisticalmethodqualitycontrol

3.30 score 7 scripts 163 downloads

CNViz - Copy Number Visualization

CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.

Last updated 2 months ago

visualizationcopynumbervariationsequencingdnaseq

3.30 score 1 scripts 164 downloads

sampleClassifier - Sample Classifier

The package is designed to classify microarray RNA-seq gene expression profiles.

Last updated 2 months ago

immunooncologyclassificationmicroarrayrnaseqgeneexpression

3.30 score 227 downloads

SeqGate - Filtering of Lowly Expressed Features

Filtering of lowly expressed features (e.g. genes) is a common step before performing statistical analysis, but an arbitrary threshold is generally chosen. SeqGate implements a method that rationalize this step by the analysis of the distibution of counts in replicate samples. The gate is the threshold above which sequenced features can be considered as confidently quantified.

Last updated 2 months ago

differentialexpressiongeneexpressiontranscriptomicssequencingrnaseq

3.30 score 3 scripts 184 downloads

pageRank - Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

Last updated 2 months ago

statisticalmethodgenetargetnetwork

3.30 score 5 scripts 162 downloads

FilterFFPE - FFPE Artificial Chimeric Read Filter for NGS data

This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.

Last updated 2 months ago

structuralvariationsequencingalignmentqualitycontrolpreprocessing

3.30 score 1 scripts 179 downloads

MultiBaC - Multiomic Batch effect Correction

MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is the first Batch effect correction algorithm that dealing with batch effect correction in multiomics datasets. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.

Last updated 2 months ago

softwarestatisticalmethodprincipalcomponentdatarepresentationgeneexpressiontranscriptionbatcheffect

3.30 score 7 scripts 316 downloads

optimalFlow - optimalFlow

Optimal-transport techniques applied to supervised flow cytometry gating.

Last updated 2 months ago

softwareflowcytometrytechnology

3.30 score 1 scripts 162 downloads

ROCpAI - Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers

The package analyzes the Curve ROC, identificates it among different types of Curve ROC and calculates the area under de curve through the method that is most accuracy. This package is able to standarizate proper and improper pAUC.

Last updated 2 months ago

softwarestatisticalmethodclassification

3.30 score 1 scripts 140 downloads

SimFFPE - NGS Read Simulator for FFPE Tissue

The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.

Last updated 2 months ago

sequencingalignmentmultiplecomparisonsequencematchingdataimport

3.30 score 1 scripts 136 downloads

RNAsense - Analysis of Time-Resolved RNA-Seq Data

RNA-sense tool compares RNA-seq time curves in two experimental conditions, i.e. wild-type and mutant, and works in three steps. At Step 1, it builds expression profile for each transcript in one condition (i.e. wild-type) and tests if the transcript abundance grows or decays significantly. Dynamic transcripts are then sorted to non-overlapping groups (time profiles) by the time point of switch up or down. At Step 2, RNA-sense outputs the groups of differentially expressed transcripts, which are up- or downregulated in the mutant compared to the wild-type at each time point. At Step 3, Correlations (Fisher's exact test) between the outputs of Step 1 (switch up- and switch down- time profile groups) and the outputs of Step2 (differentially expressed transcript groups) are calculated. The results of the correlation analysis are printed as two-dimensional color plot, with time profiles and differential expression groups at y- and x-axis, respectively, and facilitates the biological interpretation of the data.

Last updated 2 months ago

rnaseqgeneexpressiondifferentialexpression

3.30 score 1 stars 2 scripts 143 downloads

calm - Covariate Assisted Large-scale Multiple testing

Statistical methods for multiple testing with covariate information. Traditional multiple testing methods only consider a list of test statistics, such as p-values. Our methods incorporate the auxiliary information, such as the lengths of gene coding regions or the minor allele frequencies of SNPs, to improve power.

Last updated 2 months ago

bayesiandifferentialexpressiongeneexpressionregressionmicroarraysequencingrnaseqmultiplecomparisongeneticsimmunooncologymetabolomicsproteomicstranscriptomics

3.30 score 2 scripts 112 downloads

fcScan - fcScan for detecting clusters of coordinates with user defined options

This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.

Last updated 2 months ago

genomeannotationclustering

3.30 score 1 scripts 315 downloads

KnowSeq - KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers, as well as to assess them through a Machine Learning approaches. Finally, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers (Gene Ontology enrichment, Pathway listing and Visualization and Evidences related to the addressed disease). Although the package allows analyzing all the data manually, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study.

Last updated 2 months ago

geneexpressiondifferentialexpressiongenesetenrichmentdataimportclassificationfeatureextractionsequencingrnaseqbatcheffectnormalizationpreprocessingqualitycontrolgeneticstranscriptomicsmicroarrayalignmentpathwayssystemsbiologygoimmunooncology

3.30 score 5 scripts 170 downloads

ADAMgui - Activity and Diversity Analysis Module Graphical User Interface

ADAMgui is a Graphical User Interface for the ADAM package. The ADAMgui package provides 2 shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It's possible, for example, to choose a specific GFAG and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and foldchange can be easily seen with aid of the plots made with GFAGpathUi function.

Last updated 2 months ago

genesetenrichmentpathwayskegg

3.30 score 1 scripts 372 downloads

RepViz - Replicate oriented Visualization of a genomic region

RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data.

Last updated 2 months ago

workflowstepvisualizationsequencingchipseqatacseqsoftwarecoveragegenomicvariation

3.30 score 1 scripts 192 downloads

PAIRADISE - PAIRADISE: Paired analysis of differential isoform expression

This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data.

Last updated 2 months ago

rnaseqdifferentialexpressionalternativesplicingstatisticalmethodimmunooncology

3.30 score 7 scripts 220 downloads

IsoCorrectoRGUI - Graphical User Interface for IsoCorrectoR

IsoCorrectoRGUI is a Graphical User Interface for the IsoCorrectoR package. IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously).

Last updated 2 months ago

softwaremetabolomicsmassspectrometrypreprocessingguiimmunooncology

3.30 score 4 scripts 133 downloads

levi - Landscape Expression Visualization Interface

The tool integrates data from biological networks with transcriptomes, displaying a heatmap with surface curves to evidence the altered regions.

Last updated 2 months ago

geneexpressionsequencingnetworksoftwarecpp

3.30 score 4 scripts 136 downloads

traviz - Trajectory functions for visualization and interpretation.

traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.

Last updated 2 months ago

geneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsvisualization

3.00 score 2 scripts 161 downloads

BufferedMatrixMethods - Microarray Data related methods that utlize BufferedMatrix objects

Microarray analysis methods that use BufferedMatrix objects

Last updated 7 days ago

infrastructure

2.95 score 324 downloads

PanViz - Integrating Multi-Omic Network Data With Summay-Level GWAS Data

This pacakge integrates data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) with summary-level genome-wide association (GWAS) data, such as that provided by the GWAS Catalog or GWAS Central databases, or a user's own study or dataset, in order to produce biological networks, termed IMONs (Integrated Multi-Omic Networks). IMONs can be used to analyse trait-specific polymorphic data within the context of biochemical and metabolic reaction networks, providing greater biological interpretability for GWAS data.

Last updated 5 days ago

genomewideassociationreactomemetabolomicssnpgraphandnetworknetworkkegg

2.95 score 3 stars 7 scripts 109 downloads

TransView - Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

Last updated 10 days ago

immunooncologydnamethylationgeneexpressiontranscriptionmicroarraysequencingchipseqrnaseqmethylseqdataimportvisualizationclusteringmultiplecomparisoncurlbzip2xz-utilszlib

2.48 score 253 downloads

GenomicRanges - Representation and manipulation of genomic intervals

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

Last updated 1 months ago

geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package

17.88 score 45 stars 1.3k dependents 14k scripts 95k downloads

clusterProfiler - A universal enrichment tool for interpreting omics data

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

Last updated 23 days ago

annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgsea

17.10 score 1.0k stars 50 dependents 11k scripts 34k downloads

SummarizedExperiment - A container (S4 class) for matrix-like assays

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

Last updated 2 months ago

geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package

17.01 score 34 stars 1.2k dependents 9.5k scripts 85k downloads

ggtree - an R package for visualization of tree and annotation data

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

Last updated 2 months ago

alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees

16.93 score 846 stars 109 dependents 5.2k scripts 36k downloads

GenomeInfoDb - Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Last updated 25 days ago

geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package

16.52 score 31 stars 1.7k dependents 1.3k scripts 114k downloads

IRanges - Foundation of integer range manipulation in Bioconductor

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

Last updated 19 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

16.17 score 22 stars 1.8k dependents 2.1k scripts 109k downloads

S4Vectors - Foundation of vector-like and list-like containers in Bioconductor

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Last updated 1 months ago

infrastructuredatarepresentationbioconductor-packagecore-package

16.10 score 18 stars 1.8k dependents 1.1k scripts 115k downloads

DESeq2 - Differential gene expression analysis based on the negative binomial distribution

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

Last updated 1 months ago

sequencingrnaseqchipseqgeneexpressiontranscriptionnormalizationdifferentialexpressionbayesianregressionprincipalcomponentclusteringimmunooncologyopenblascpp

16.00 score 365 stars 118 dependents 16k scripts 37k downloads

treeio - Base Classes and Functions for Phylogenetic Tree Input and Output

'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

Last updated 2 months ago

softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees

15.02 score 97 stars 122 dependents 1.3k scripts 32k downloads

maftools - Summarize, Analyze and Visualize MAF Files

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Last updated 2 months ago

datarepresentationdnaseqvisualizationdrivermutationvariantannotationfeatureextractionclassificationsomaticmutationsequencingfunctionalgenomicssurvivalbioinformaticscancer-genome-atlascancer-genomicsgenomicsmaf-filestcgacurlbzip2xz-utilszlib

14.68 score 452 stars 18 dependents 884 scripts 4.0k downloads

BiocFileCache - Manage Files Across Sessions

This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

Last updated 2 months ago

dataimportcore-package

13.65 score 12 stars 429 dependents 478 scripts 45k downloads

RCy3 - Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Last updated 2 months ago

visualizationgraphandnetworkthirdpartyclientnetwork

13.39 score 52 stars 16 dependents 600 scripts 1.5k downloads

scran - Methods for Single-Cell RNA-Seq Data Analysis

Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.

Last updated 2 months ago

immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellclusteringbioconductor-packagehuman-cell-atlassingle-cell-rna-seqopenblascpp

13.19 score 40 stars 35 dependents 7.5k scripts 8.3k downloads

MAST - Model-based Analysis of Single Cell Transcriptomics

Methods and models for handling zero-inflated single cell assay data.

Last updated 2 months ago

geneexpressiondifferentialexpressiongenesetenrichmentrnaseqtranscriptomicssinglecell

12.75 score 228 stars 5 dependents 1.8k scripts 3.3k downloads

plyranges - A fluent interface for manipulating GenomicRanges

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

Last updated 2 months ago

infrastructuredatarepresentationworkflowstepcoveragebioconductordata-analysisdplyrgenomic-rangesgenomicstidy-data

12.58 score 142 stars 20 dependents 1.9k scripts 1.8k downloads

TCGAbiolinks - TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

Last updated 2 months ago

dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksequencingsurvivalsoftwarebiocbioconductorgdcintegrative-analysistcgatcga-datatcgabiolinks

12.51 score 300 stars 6 dependents 1.6k scripts 6.9k downloads

microbiome - Microbiome Analytics

Utilities for microbiome analysis.

Last updated 2 months ago

metagenomicsmicrobiomesequencingsystemsbiologyhitchiphitchip-atlashuman-microbiomemicrobiologymicrobiome-analysisphyloseqpopulation-study

12.49 score 289 stars 5 dependents 1.8k scripts 2.6k downloads

EnhancedVolcano - Publication-ready volcano plots with enhanced colouring and labeling

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.

Last updated 2 months ago

rnaseqgeneexpressiontranscriptiondifferentialexpressionimmunooncology

12.12 score 415 stars 1 dependents 2.6k scripts 6.8k downloads

slingshot - Tools for ordering single-cell sequencing

Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

Last updated 2 months ago

clusteringdifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsvisualization

11.99 score 274 stars 4 dependents 1.0k scripts 2.6k downloads

DelayedMatrixStats - Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects

A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

Last updated 2 months ago

infrastructuredatarepresentationsoftware

11.77 score 15 stars 114 dependents 203 scripts 28k downloads

GenomicDataCommons - NIH / NCI Genomic Data Commons Access

Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

Last updated 2 months ago

dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette

11.69 score 84 stars 10 dependents 190 scripts 1.6k downloads

PharmacoGx - Analysis of Large-Scale Pharmacogenomic Data

Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

Last updated 2 months ago

geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogxcpp

11.62 score 67 stars 3 dependents 381 scripts 554 downloads

karyoploteR - Plot customizable linear genomes displaying arbitrary data

karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

Last updated 2 months ago

visualizationcopynumbervariationsequencingcoveragednaseqchipseqmethylseqdataimportonechannelbioconductorbioinformaticsdata-visualizationgenomegenomics-visualizationplotting-in-r

11.41 score 299 stars 4 dependents 646 scripts 1.5k downloads

Rhdf5lib - hdf5 library as an R package

Provides C and C++ hdf5 libraries.

Last updated 2 months ago

infrastructurebioconductorhdf5hdf5-libraryfortranzlib

11.38 score 6 stars 340 dependents 24 scripts 41k downloads

decontam - Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.

Last updated 2 months ago

immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioinformaticscontaminationmetabarcoding

11.34 score 149 stars 5 dependents 498 scripts 2.5k downloads

tximeta - Transcript Quantification Import with Automatic Metadata

Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

Last updated 2 months ago

annotationgenomeannotationdataimportpreprocessingrnaseqsinglecelltranscriptomicstranscriptiongeneexpressionfunctionalgenomicsreproducibleresearchreportwritingimmunooncology

10.62 score 67 stars 1 dependents 450 scripts 2.0k downloads

zinbwave - Zero-Inflated Negative Binomial Model for RNA-Seq Data

Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.

Last updated 2 months ago

immunooncologydimensionreductiongeneexpressionrnaseqsoftwaretranscriptomicssequencingsinglecell

10.53 score 43 stars 6 dependents 190 scripts 1.6k downloads

BASiCS - Bayesian Analysis of Single-Cell Sequencing data

Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.

Last updated 2 months ago

immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecelldifferentialexpressionbayesiancellbiologybioconductor-packagegene-expressionrcpprcpparmadilloscrna-seqsingle-cellopenblascppopenmp

10.36 score 84 stars 1 dependents 366 scripts 405 downloads

AnnotationFilter - Facilities for Filtering Bioconductor Annotation Resources

This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

Last updated 2 months ago

annotationinfrastructuresoftwarebioconductor-packagecore-package

10.19 score 5 stars 163 dependents 44 scripts 18k downloads

Glimma - Interactive visualizations for gene expression analysis

This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.

Last updated 2 months ago

differentialexpressiongeneexpressionmicroarrayreportwritingrnaseqsequencingvisualizationdifferential-expressioninteractive-visualizations

10.10 score 25 stars 2 dependents 564 scripts 1.7k downloads

singscore - Rank-based single-sample gene set scoring method

A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample's gene expression profile. It scores the expression activities of gene sets at a single-sample level.

Last updated 2 months ago

softwaregeneexpressiongenesetenrichmentbioinformatics

9.88 score 40 stars 3 dependents 117 scripts 2.3k downloads

diffcyt - Differential discovery in high-dimensional cytometry via high-resolution clustering

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.

Last updated 2 months ago

immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware

9.76 score 19 stars 5 dependents 225 scripts 903 downloads

annotatr - Annotation of Genomic Regions to Genomic Annotations

Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.

Last updated 2 months ago

softwareannotationgenomeannotationfunctionalgenomicsvisualizationgenome-annotation

9.76 score 25 stars 5 dependents 254 scripts 837 downloads

PureCN - Copy number calling and SNV classification using targeted short read sequencing

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Last updated 2 months ago

copynumbervariationsoftwaresequencingvariantannotationvariantdetectioncoverageimmunooncologybioconductor-packagecell-free-dnacopy-numberlohtumor-heterogeneitytumor-mutational-burdentumor-purity

9.71 score 128 stars 52 scripts 406 downloads

clusterExperiment - Compare Clusterings for Single-Cell Sequencing

Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.

Last updated 2 months ago

clusteringrnaseqsequencingsoftwaresinglecellcpp

9.60 score 37 stars 1 dependents 188 scripts 734 downloads

RcisTarget - RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

Last updated 2 months ago

generegulationmotifannotationtranscriptomicstranscriptiongenesetenrichmentgenetarget

9.45 score 34 stars 192 scripts 1.8k downloads

LOLA - Locus overlap analysis for enrichment of genomic ranges

Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.

Last updated 2 months ago

genesetenrichmentgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqmethylseqsequencing

9.32 score 72 stars 163 scripts 433 downloads

IsoformSwitchAnalyzeR - Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

Last updated 2 months ago

geneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicingvisualizationstatisticalmethodtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologytranscriptomicsrnaseqannotationfunctionalpredictiongenepredictiondataimportmultiplecomparisonbatcheffectimmunooncology

9.23 score 103 stars 122 scripts 593 downloads

rWikiPathways - rWikiPathways - R client library for the WikiPathways API

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.

Last updated 2 months ago

visualizationgraphandnetworkthirdpartyclientnetworkmetabolomicsbioinformaticsdata-accesspathways

9.21 score 15 stars 3 dependents 124 scripts 739 downloads

CytoML - A GatingML Interface for Cross Platform Cytometry Data Sharing

Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

Last updated 2 months ago

immunooncologyflowcytometrydataimportdatarepresentationzlibopenblaslibxml2cpp

9.07 score 30 stars 130 scripts 942 downloads

OUTRIDER - OUTRIDER - OUTlier in RNA-Seq fInDER

Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.

Last updated 2 months ago

immunooncologyrnaseqtranscriptomicsalignmentsequencinggeneexpressiongeneticscount-datadiagnosticsexpression-analysismendelian-geneticsoutlier-detectionrna-seqopenblascpp

9.06 score 49 stars 1 dependents 109 scripts 358 downloads

scone - Single Cell Overview of Normalized Expression data

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

Last updated 2 months ago

immunooncologynormalizationpreprocessingqualitycontrolgeneexpressionrnaseqsoftwaretranscriptomicssequencingsinglecellcoverage

9.00 score 53 stars 104 scripts 373 downloads

motifbreakR - A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 32 species, a total of 109 versions).

Last updated 2 months ago

chipseqvisualizationmotifannotationtranscription

8.94 score 28 stars 98 scripts 477 downloads

BatchQC - Batch Effects Quality Control Software

Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.

Last updated 2 months ago

batcheffectgraphandnetworkmicroarraynormalizationprincipalcomponentsequencingsoftwarevisualizationqualitycontrolrnaseqpreprocessingdifferentialexpressionimmunooncology

8.91 score 6 stars 53 scripts 244 downloads

progeny - Pathway RespOnsive GENes for activity inference from gene expression

PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.

Last updated 2 months ago

systemsbiologygeneexpressionfunctionalpredictiongeneregulation

8.91 score 93 stars 1 dependents 245 scripts 903 downloads

RTCGA - The Cancer Genome Atlas Data Integration

The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.

Last updated 2 months ago

immunooncologysoftwaredataimportdatarepresentationpreprocessingrnaseqsurvivaldnamethylationprincipalcomponentvisualization

8.91 score 51 stars 1 dependents 106 scripts 925 downloads

AUCell - AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

Last updated 2 months ago

singlecellgenesetenrichmenttranscriptomicstranscriptiongeneexpressionworkflowstepnormalization

8.89 score 4 dependents 820 scripts 3.9k downloads

scmap - A tool for unsupervised projection of single cell RNA-seq data

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.

Last updated 2 months ago

immunooncologysinglecellsoftwareclassificationsupportvectormachinernaseqvisualizationtranscriptomicsdatarepresentationtranscriptionsequencingpreprocessinggeneexpressiondataimportbioconductor-packagehuman-cell-atlasprojection-mappingsingle-cell-rna-seqopenblascpp

8.79 score 90 stars 172 scripts 560 downloads

drawProteins - Package to Draw Protein Schematics from Uniprot API output

This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.

Last updated 2 months ago

visualizationfunctionalpredictionproteomics

8.73 score 34 stars 1 dependents 59 scripts 314 downloads

M3Drop - Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model.

Last updated 2 months ago

rnaseqsequencingtranscriptomicsgeneexpressionsoftwaredifferentialexpressiondimensionreductionfeatureextractionhuman-cell-atlasrna-seqsingle-cellsingle-cell-rna-seq

8.70 score 29 stars 2 dependents 117 scripts 1.0k downloads

GenomicScores - Infrastructure to work with genomewide position-specific scores

Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

Last updated 2 months ago

infrastructuregeneticsannotationsequencingcoverageannotationhubsoftware

8.70 score 8 stars 6 dependents 83 scripts 1.2k downloads

apeglm - Approximate posterior estimation for GLM coefficients

apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.

Last updated 2 months ago

immunooncologysequencingrnaseqdifferentialexpressiongeneexpressionbayesiancpp

8.63 score 9 dependents 680 scripts 5.9k downloads

HiCcompare - HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

Last updated 2 months ago

softwarehicsequencingnormalizationdifference-detectionhi-cvisualization

8.56 score 19 stars 5 dependents 45 scripts 459 downloads

SIMLR - Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)

Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical for the identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization.

Last updated 2 months ago

immunooncologyclusteringgeneexpressionsequencingsinglecell

8.47 score 109 stars 68 scripts 348 downloads

SCnorm - Normalization of single cell RNA-seq data

This package implements SCnorm — a method to normalize single-cell RNA-seq data.

Last updated 2 months ago

normalizationrnaseqsinglecellimmunooncology

8.46 score 47 stars 76 scripts 286 downloads

multiMiR - Integration of multiple microRNA-target databases with their disease and drug associations

A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).

Last updated 2 months ago

mirnadatahomo_sapiens_datamus_musculus_datarattus_norvegicus_dataorganismdatamicrorna-sequencesql

8.44 score 20 stars 139 scripts 402 downloads

BgeeDB - Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

Last updated 2 months ago

softwaredataimportsequencinggeneexpressionmicroarraygogenesetenrichmentbioinformaticsenrichment-analysisrna-seqscrna-seqsingle-cell

8.41 score 14 stars 1 dependents 18 scripts 410 downloads

igvR - igvR: integrative genomics viewer

Access to igv.js, the Integrative Genomics Viewer running in a web browser.

Last updated 2 months ago

visualizationthirdpartyclientgenomebrowsers

8.31 score 43 stars 118 scripts 281 downloads

DEqMS - a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.

Last updated 2 months ago

immunooncologyproteomicsmassspectrometrypreprocessingdifferentialexpressionmultiplecomparisonnormalizationbayesianexperimenthubsoftwarelimmaquantitative-proteomic-analysis

8.16 score 22 stars 1 dependents 58 scripts 385 downloads

IPO - Automated Optimization of XCMS Data Processing parameters

The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.

Last updated 2 months ago

immunooncologymetabolomicsmassspectrometry

8.13 score 34 stars 40 scripts 439 downloads

motifmatchr - Fast Motif Matching in R

Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.

Last updated 2 months ago

motifannotationcpp

8.11 score 5 dependents 706 scripts 2.4k downloads

debrowser - Interactive Differential Expresion Analysis Browser

Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.

Last updated 2 months ago

sequencingchipseqrnaseqdifferentialexpressiongeneexpressionclusteringimmunooncology

8.08 score 60 stars 63 scripts 345 downloads

philr - Phylogenetic partitioning based ILR transform for metagenomics data

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

Last updated 2 months ago

immunooncologysequencingmicrobiomemetagenomicssoftware

8.04 score 19 stars 108 scripts 330 downloads

InteractionSet - Base Classes for Storing Genomic Interaction Data

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

Last updated 2 months ago

infrastructuredatarepresentationsoftwarehiccpp

7.96 score 36 dependents 247 scripts 2.9k downloads

scDD - Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

Last updated 2 months ago

immunooncologybayesianclusteringrnaseqsinglecellmultiplecomparisonvisualizationdifferentialexpression

7.90 score 32 stars 50 scripts 396 downloads

phantasus - Visual and interactive gene expression analysis

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

Last updated 2 months ago

geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology

7.71 score 43 stars 15 scripts 470 downloads

AneuFinder - Analysis of Copy Number Variation in Single-Cell-Sequencing Data

AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.

Last updated 2 months ago

immunooncologysoftwaresequencingsinglecellcopynumbervariationgenomicvariationhiddenmarkovmodelwholegenomecpp

7.70 score 17 stars 37 scripts 424 downloads

ropls - PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).

Last updated 2 months ago

regressionclassificationprincipalcomponenttranscriptomicsproteomicsmetabolomicslipidomicsmassspectrometryimmunooncology

7.69 score 8 dependents 191 scripts 1.8k downloads

coRdon - Codon Usage Analysis and Prediction of Gene Expressivity

Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.

Last updated 2 months ago

softwaremetagenomicsgeneexpressiongenesetenrichmentgenepredictionvisualizationkeggpathwaysgenetics cellbiologybiomedicalinformaticsimmunooncology

7.68 score 19 stars 1 dependents 47 scripts 290 downloads

signeR - Empirical Bayesian approach to mutational signature discovery

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

Last updated 2 months ago

genomicvariationsomaticmutationstatisticalmethodvisualizationbioconductorbioinformaticsopenblascpp

7.67 score 13 stars 22 scripts 216 downloads

amplican - Automated analysis of CRISPR experiments

`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.

Last updated 2 months ago

immunooncologytechnologyalignmentqpcrcrisprcpp

7.66 score 10 stars 41 scripts 346 downloads

GENIE3 - GEne Network Inference with Ensemble of trees

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

Last updated 2 months ago

networkinferencesystemsbiologydecisiontreeregressionnetworkgraphandnetworkgeneexpression

7.58 score 4 dependents 164 scripts 1.9k downloads

MIRA - Methylation-Based Inference of Regulatory Activity

DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.

Last updated 2 months ago

immunooncologydnamethylationgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqmethylseqsequencingepigeneticscoverage

7.52 score 11 stars 1 dependents 7 scripts 218 downloads

CAGEfightR - Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Last updated 2 months ago

softwaretranscriptioncoveragegeneexpressiongeneregulationpeakdetectiondataimportdatarepresentationtranscriptomicssequencingannotationgenomebrowsersnormalizationpreprocessingvisualization

7.45 score 8 stars 1 dependents 65 scripts 530 downloads

HilbertCurve - Making 2D Hilbert Curve

Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.

Last updated 2 months ago

softwarevisualizationsequencingcoveragegenomeannotationcpp

7.44 score 41 stars 48 scripts 257 downloads

netSmooth - Network smoothing for scRNAseq

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.

Last updated 2 months ago

networkgraphandnetworksinglecellrnaseqgeneexpressionsequencingtranscriptomicsnormalizationpreprocessingclusteringdimensionreductionbioinformaticsgenomicssingle-cell

7.41 score 27 stars 4 scripts 212 downloads

DEsingle - DEsingle for detecting three types of differential expression in single-cell RNA-seq data

DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results showed that DEsingle outperforms existing methods for scRNA-seq DE analysis, and can reveal different types of DE genes that are enriched in different biological functions.

Last updated 2 months ago

differentialexpressiongeneexpressionsinglecellimmunooncologyrnaseqtranscriptomicssequencingpreprocessingsoftware

7.40 score 30 stars 28 scripts 517 downloads

sevenbridges - Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.

Last updated 2 months ago

softwaredataimportthirdpartyclientapi-clientbioconductorbioinformaticscloudcommon-workflow-languagesevenbridges

7.40 score 35 stars 24 scripts 198 downloads

HPAanalyze - Retrieve and analyze data from the Human Protein Atlas

Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data.

Last updated 2 months ago

proteomicscellbiologyvisualizationsoftware

7.40 score 32 stars 37 scripts 252 downloads

diffcoexp - Differential Co-expression Analysis

A tool for the identification of differentially coexpressed links (DCLs) and differentially coexpressed genes (DCGs). DCLs are gene pairs with significantly different correlation coefficients under two conditions. DCGs are genes with significantly more DCLs than by chance.

Last updated 2 months ago

geneexpressiondifferentialexpressiontranscriptionmicroarrayonechanneltwochannelrnaseqsequencingcoverageimmunooncology

7.37 score 15 stars 1 dependents 37 scripts 339 downloads

ELMER - Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Last updated 2 months ago

dnamethylationgeneexpressionmotifannotationsoftwaregeneregulationtranscriptionnetwork

7.36 score 154 scripts 380 downloads

chromVAR - Chromatin Variation Across Regions

Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.

Last updated 2 months ago

singlecellsequencinggeneregulationimmunooncologycpp

7.30 score 756 scripts 2.6k downloads

cytolib - C++ infrastructure for representing and interacting with the gated cytometry data

This package provides the core data structure and API to represent and interact with the gated cytometry data.

Last updated 2 months ago

immunooncologyflowcytometrydataimportpreprocessingdatarepresentation

7.28 score 60 dependents 7 scripts 4.3k downloads

MutationalPatterns - Comprehensive genome-wide analysis of mutational processes

Mutational processes leave characteristic footprints in genomic DNA. This package provides a comprehensive set of flexible functions that allows researchers to easily evaluate and visualize a multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. The package covers a wide range of patterns including: mutational signatures, transcriptional and replicative strand bias, lesion segregation, genomic distribution and association with genomic features, which are collectively meaningful for studying the activity of mutational processes. The package works with single nucleotide variants (SNVs), insertions and deletions (Indels), double base substitutions (DBSs) and larger multi base substitutions (MBSs). The package provides functionalities for both extracting mutational signatures de novo and determining the contribution of previously identified mutational signatures on a single sample level. MutationalPatterns integrates with common R genomic analysis workflows and allows easy association with (publicly available) annotation data.

Last updated 2 months ago

geneticssomaticmutation

7.28 score 1 dependents 255 scripts 636 downloads

NormalyzerDE - Evaluation of normalization methods and calculation of differential expression analysis statistics

NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.

Last updated 2 months ago

normalizationmultiplecomparisonvisualizationbayesianproteomicsmetabolomicsdifferentialexpressionbioconductorbioinformaticslimma

7.26 score 20 stars 1 dependents 38 scripts 350 downloads

multiHiCcompare - Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

Last updated 2 months ago

softwarehicsequencingnormalization

7.25 score 8 stars 2 dependents 37 scripts 324 downloads

meshes - MeSH Enrichment and Semantic analyses

MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.

Last updated 2 months ago

annotationclusteringmultiplecomparisonsoftwareenrichment-analysismedical-subject-headingssemantic-similarity

7.25 score 11 stars 43 scripts 355 downloads

glmSparseNet - Network Centrality Metrics for Elastic-Net Regularized Models

glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".

Last updated 2 months ago

softwarestatisticalmethoddimensionreductionregressionclassificationsurvivalnetworkgraphandnetwork

7.20 score 6 stars 37 scripts 415 downloads

psichomics - Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Last updated 2 months ago

sequencingrnaseqalternativesplicingdifferentialsplicingtranscriptionguiprincipalcomponentsurvivalbiomedicalinformaticstranscriptomicsimmunooncologyvisualizationmultiplecomparisongeneexpressiondifferentialexpressionalternative-splicingbioconductordata-analysesdifferential-gene-expressiondifferential-splicing-analysisgene-expressiongtexrecount2rna-seq-datasplicing-quantificationsratcgavast-toolscpp

7.13 score 36 stars 31 scripts 218 downloads

isomiRs - Analyze isomiRs and miRNAs from small RNA-seq

Characterization of miRNAs and isomiRs, clustering and differential expression.

Last updated 2 months ago

mirnarnaseqdifferentialexpressionclusteringimmunooncologyanalyze-isomirsbioconductorisomirs

7.05 score 8 stars 39 scripts 309 downloads

ATACseqQC - ATAC-seq Quality Control

ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.

Last updated 2 months ago

sequencingdnaseqatacseqgeneregulationqualitycontrolcoveragenucleosomepositioningimmunooncology

7.04 score 1 dependents 146 scripts 870 downloads

RProtoBufLib - C++ headers and static libraries of Protocol buffers

This package provides the headers and static library of Protocol buffers for other R packages to compile and link against.

Last updated 2 months ago

infrastructure

7.04 score 61 dependents 4.0k downloads

msPurity - Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.

Last updated 2 months ago

massspectrometrymetabolomicssoftwarebioconductor-packagedimsfragmentationlc-mslc-msmsmass-spectrometryprecursor-ion-purity

7.03 score 15 stars 44 scripts 234 downloads

DEP - Differential Enrichment analysis of Proteomics data

This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant. Functions are provided for data preparation, filtering, variance normalization and imputation of missing values, as well as statistical testing of differentially enriched / expressed proteins. It also includes tools to check intermediate steps in the workflow, such as normalization and missing values imputation. Finally, visualization tools are provided to explore the results, including heatmap, volcano plot and barplot representations. For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report. Even easier to use are the interactive Shiny apps that are provided by the package.

Last updated 2 months ago

immunooncologyproteomicsmassspectrometrydifferentialexpressiondatarepresentation

7.03 score 534 scripts 912 downloads

ACE - Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.

Last updated 2 months ago

copynumbervariationdnaseqcoveragewholegenomevisualizationsequencing

7.00 score 14 stars 18 scripts 310 downloads

DRIMSeq - Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.

Last updated 2 months ago

immunooncologysnpalternativesplicingdifferentialsplicinggeneticsrnaseqsequencingworkflowstepmultiplecomparisongeneexpressiondifferentialexpression

6.90 score 2 dependents 133 scripts 617 downloads

methylGSA - Gene Set Analysis Using the Outcome of Differential Methylation

The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.

Last updated 2 months ago

dnamethylationdifferentialmethylationgenesetenrichmentregressiongeneregulationpathwaysenrichmentgeneralized-linear-modelslogistic-regressionmethylationontologyshiny

6.90 score 11 stars 36 scripts 276 downloads

SIAMCAT - Statistical Inference of Associations between Microbial Communities And host phenoTypes

Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).

Last updated 2 months ago

immunooncologymetagenomicsclassificationmicrobiomesequencingpreprocessingclusteringfeatureextractiongeneticvariabilitymultiplecomparisonregression

6.90 score 110 scripts 297 downloads

onlineFDR - Online error rate control

This package allows users to control the false discovery rate (FDR) or familywise error rate (FWER) for online multiple hypothesis testing, where hypotheses arrive in a stream. In this framework, a null hypothesis is rejected based on the evidence against it and on the previous rejection decisions.

Last updated 2 months ago

multiplecomparisonsoftwarestatisticalmethoderror-rate-controlfdrfwerhypothesis-testingcpp

6.87 score 14 stars 25 scripts 105 downloads

DEFormats - Differential gene expression data formats converter

Convert between different data formats used by differential gene expression analysis tools.

Last updated 2 months ago

immunooncologydifferentialexpressiongeneexpressionrnaseqsequencingtranscription

6.82 score 4 stars 1 dependents 78 scripts 429 downloads

Organism.dplyr - dplyr-based Access to Bioconductor Annotation Resources

This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

Last updated 2 months ago

annotationsequencinggenomeannotationbioconductor-packagecore-package

6.79 score 3 stars 1 dependents 66 scripts 739 downloads

chimeraviz - Visualization tools for gene fusions

chimeraviz manages data from fusion gene finders and provides useful visualization tools.

Last updated 2 months ago

infrastructurealignment

6.71 score 37 stars 14 scripts 288 downloads

SPONGE - Sparse Partial Correlations On Gene Expression

This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Last updated 2 months ago

geneexpressiontranscriptiongeneregulationnetworkinferencetranscriptomicssystemsbiologyregressionrandomforestmachinelearning

6.66 score 1 dependents 38 scripts 134 downloads

GDSArray - Representing GDS files as array-like objects

GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.

Last updated 2 months ago

infrastructuredatarepresentationsequencinggenotypingarray

6.65 score 5 stars 2 dependents 8 scripts 498 downloads

BioCor - Functional similarities

Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...

Last updated 2 months ago

statisticalmethodclusteringgeneexpressionnetworkpathwaysnetworkenrichmentsystemsbiologybioconductor-packagesbioinformaticsfunctional-similaritygenegene-setspathway-analysissimilaritysimilarity-measurement

6.59 score 14 stars 330 downloads

vidger - Create rapid visualizations of RNAseq data in R

The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.

Last updated 2 months ago

immunooncologyvisualizationrnaseqdifferentialexpressiongeneexpressiondata-mungingdifferential-expressiongene-expressionrna-seq-analysis

6.59 score 18 stars 27 scripts 275 downloads

M3C - Monte Carlo Reference-based Consensus Clustering

M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of K and can reject the null hypothesis K=1.

Last updated 2 months ago

clusteringgeneexpressiontranscriptionrnaseqsequencingimmunooncology

6.59 score 1 dependents 175 scripts 1.1k downloads

MoonlightR - Identify oncogenes and tumor suppressor genes from omics data

Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.

Last updated 2 months ago

dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksurvivalgenesetenrichmentnetworkenrichment

6.57 score 17 stars 224 downloads

LOBSTAHS - Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.

Last updated 2 months ago

immunooncologymassspectrometrymetabolomicslipidomicsdataimportadductalgaebioconductorhplc-esi-mslipidmass-spectrometryoxidative-stress-biomarkersoxidized-lipidsoxylipinsplankton

6.56 score 8 stars 9 scripts 245 downloads

GSEABenchmarkeR - Reproducible GSEA Benchmarking

The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.

Last updated 2 months ago

immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwritingbioconductor-package

6.55 score 13 stars 23 scripts 237 downloads

Trendy - Breakpoint analysis of time-course expression data

Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions.

Last updated 2 months ago

timecoursernaseqregressionimmunooncology

6.53 score 6 stars 14 scripts 212 downloads

MultiDataSet - Implementation of MultiDataSet and ResultSet

Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.

Last updated 2 months ago

softwaredatarepresentation

6.52 score 11 dependents 28 scripts 1.8k downloads

miRBaseConverter - A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions

A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.

Last updated 2 months ago

softwaremirna

6.50 score 1 stars 70 scripts 196 downloads

dmrseq - Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.

Last updated 2 months ago

immunooncologydnamethylationepigeneticsmultiplecomparisonsoftwaresequencingdifferentialmethylationwholegenomeregressionfunctionalgenomics

6.46 score 1 dependents 55 scripts 594 downloads

RCAS - RNA Centric Annotation System

RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses and discriminative motif discovery.

Last updated 2 months ago

softwaregenetargetmotifannotationmotifdiscoverygotranscriptomicsgenomeannotationgenesetenrichmentcoverage

6.44 score 1 dependents 29 scripts 384 downloads

ndexr - NDEx R client library

This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.

Last updated 2 months ago

pathwaysdataimportnetwork

6.44 score 9 stars 38 scripts 172 downloads

YAPSA - Yet Another Package for Signature Analysis

This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.

Last updated 2 months ago

sequencingdnaseqsomaticmutationvisualizationclusteringgenomicvariationstatisticalmethodbiologicalquestion

6.41 score 57 scripts 426 downloads

gwasurvivr - gwasurvivr: an R package for genome wide survival analysis

gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.

Last updated 2 months ago

genomewideassociationsurvivalregressiongeneticssnpgeneticvariabilitypharmacogenomicsbiomedicalinformatics

6.39 score 11 stars 75 scripts 286 downloads

SparseSignatures - SparseSignatures

Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient's tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.

Last updated 2 months ago

biomedicalinformaticssomaticmutation

6.38 score 10 stars 4 scripts 205 downloads

Linnorm - Linear model and normality based normalization and transformation method (Linnorm)

Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.

Last updated 2 months ago

immunooncologysequencingchipseqrnaseqdifferentialexpressiongeneexpressiongeneticsnormalizationsoftwaretranscriptionbatcheffectpeakdetectionclusteringnetworksinglecellcpp

6.26 score 5 dependents 61 scripts 460 downloads

flowPloidy - Analyze flow cytometer data to determine sample ploidy

Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.

Last updated 2 months ago

flowcytometryguiregressionvisualizationbioconductorevolutionflow-cytometrypolyploidy

6.26 score 5 stars 5 scripts 191 downloads

swfdr - Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates

This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the false discovery rate conditional on covariates, using a regression framework, as per Boca and Leek, "A direct approach to estimating false discovery rates conditional on covariates," 2018, PeerJ.

Last updated 2 months ago

multiplecomparisonstatisticalmethodsoftware

6.25 score 3 stars 37 scripts 224 downloads

OmaDB - R wrapper for the OMA REST API

A package for the orthology prediction data download from OMA database.

Last updated 2 months ago

softwarecomparativegenomicsfunctionalgenomicsgeneticsannotationgofunctionalprediction

6.23 score 2 stars 5 scripts 488 downloads

scruff - Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.

Last updated 2 months ago

softwaretechnologysequencingalignmentrnaseqsinglecellworkflowsteppreprocessingqualitycontrolvisualizationimmunooncologybioinformaticsscrna-seqsingle-cellumi

6.20 score 8 stars 22 scripts 197 downloads

martini - GWAS Incorporating Networks

martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.

Last updated 2 months ago

softwaregenomewideassociationsnpgeneticvariabilitygeneticsfeatureextractiongraphandnetworknetworkbioinformaticsgenomicsgwasnetwork-analysissnpssystems-biologycpp

6.16 score 4 stars 30 scripts 208 downloads

kissDE - Retrieves Condition-Specific Variants in RNA-Seq Data

Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data.

Last updated 2 months ago

alternativesplicingdifferentialsplicingexperimentaldesigngenomicvariationrnaseqtranscriptomics

6.16 score 3 stars 7 scripts 218 downloads

OncoScore - A tool to identify potentially oncogenic genes

OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.

Last updated 2 months ago

biomedicalinformatics

6.15 score 5 stars 2 scripts 236 downloads

mpra - Analyze massively parallel reporter assays

Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).

Last updated 2 months ago

softwaregeneregulationsequencingfunctionalgenomics

6.14 score 5 stars 13 scripts 212 downloads

esATAC - An Easy-to-use Systematic pipeline for ATACseq data analysis

This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.

Last updated 2 months ago

immunooncologysequencingdnaseqqualitycontrolalignmentpreprocessingcoverageatacseqdnaseseqatac-seqbioconductorpipelinecppopenjdk

6.11 score 23 stars 3 scripts 236 downloads

seqcombo - Visualization Tool for Genetic Reassortment

Provides useful functions for visualizing virus reassortment events.

Last updated 2 months ago

alignmentsoftwarevisualization

6.10 score 21 stars 4 scripts 175 downloads

QUBIC - An R package for qualitative biclustering in support of gene co-expression analyses

The core function of this R package is to provide the implementation of the well-cited and well-reviewed QUBIC algorithm, aiming to deliver an effective and efficient biclustering capability. This package also includes the following related functions: (i) a qualitative representation of the input gene expression data, through a well-designed discretization way considering the underlying data property, which can be directly used in other biclustering programs; (ii) visualization of identified biclusters using heatmap in support of overall expression pattern analysis; (iii) bicluster-based co-expression network elucidation and visualization, where different correlation coefficient scores between a pair of genes are provided; and (iv) a generalize output format of biclusters and corresponding network can be freely downloaded so that a user can easily do following comprehensive functional enrichment analysis (e.g. DAVID) and advanced network visualization (e.g. Cytoscape).

Last updated 2 months ago

statisticalmethodmicroarraydifferentialexpressionmultiplecomparisonclusteringvisualizationgeneexpressionnetworkbioconductor-packagebioconductor-packagescppopenmp

6.10 score 3 stars 1 dependents 14 scripts 255 downloads

EGSEA - Ensemble of Gene Set Enrichment Analyses

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set.

Last updated 2 months ago

immunooncologydifferentialexpressiongogeneexpressiongenesetenrichmentgeneticsmicroarraymultiplecomparisononechannelpathwaysrnaseqsequencingsoftwaresystemsbiologytwochannelmetabolomicsproteomicskegggraphandnetworkgenesignalinggenetargetnetworkenrichmentnetworkclassification

6.09 score 62 scripts 512 downloads

ramwas - Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) <doi:10.1093/bioinformatics/bty069>.

Last updated 2 months ago

dnamethylationsequencingqualitycontrolcoveragepreprocessingnormalizationbatcheffectprincipalcomponentdifferentialmethylationvisualization

6.08 score 10 stars 85 scripts 265 downloads

discordant - The Discordant Method: A Novel Approach for Differential Correlation

Discordant is an R package that identifies pairs of features that correlate differently between phenotypic groups, with application to -omics data sets. Discordant uses a mixture model that “bins” molecular feature pairs based on their type of coexpression or coabbundance. Algorithm is explained further in "Differential Correlation for Sequencing Data"" (Siska et al. 2016).

Last updated 2 months ago

immunooncologybiologicalquestionstatisticalmethodmrnamicroarraymicroarraygeneticsrnaseqcpp

6.05 score 10 stars 14 scripts 228 downloads

EventPointer - An effective identification of alternative splicing events using junction arrays and RNA-Seq data

EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.

Last updated 2 months ago

alternativesplicingdifferentialsplicingmrnamicroarrayrnaseqtranscriptionsequencingtimecourseimmunooncology

6.00 score 4 stars 6 scripts 250 downloads

switchde - Switch-like differential expression across single-cell trajectories

Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.

Last updated 2 months ago

immunooncologysoftwaretranscriptomicsgeneexpressionrnaseqregressiondifferentialexpressionsinglecellgene-expressiongenomicssingle-cell

5.98 score 19 stars 7 scripts 185 downloads

consensusOV - Gene expression-based subtype classification for high-grade serous ovarian cancer

This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.

Last updated 2 months ago

classificationclusteringdifferentialexpressiongeneexpressionmicroarraytranscriptomicscancer-datacancer-genomicscancer-researchexpression-databaseovarian-cancer

5.98 score 2 stars 1 dependents 15 scripts 265 downloads

bioCancer - Interactive Multi-Omics Cancers Data Visualization and Analysis

This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.

Last updated 2 months ago

guidatarepresentationnetworkmultiplecomparisonpathwaysreactomevisualizationgeneexpressiongenetargetanalysisbiocancer-interfacecancercancer-studiesrmarkdown

5.95 score 20 stars 7 scripts 201 downloads

epivizrServer - WebSocket server infrastructure for epivizr apps and packages

This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.

Last updated 2 months ago

infrastructurevisualization

5.95 score 5 dependents 6 scripts 245 downloads

zFPKM - A suite of functions to facilitate zFPKM transformations

Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.

Last updated 2 months ago

immunooncologyrnaseqfeatureextractionsoftwaregeneexpression

5.94 score 9 stars 16 scripts 372 downloads

REMP - Repetitive Element Methylation Prediction

Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.

Last updated 2 months ago

dnamethylationmicroarraymethylationarraysequencinggenomewideassociationepigeneticspreprocessingmultichanneltwochanneldifferentialmethylationqualitycontroldataimport

5.94 score 2 stars 18 scripts 214 downloads

normr - Normalization and difference calling in ChIP-seq data

Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.

Last updated 2 months ago

bayesiandifferentialpeakcallingclassificationdataimportchipseqripseqfunctionalgenomicsgeneticsmultiplecomparisonnormalizationpeakdetectionpreprocessingalignmentcppopenmp

5.93 score 11 stars 13 scripts 288 downloads

TissueEnrich - Tissue-specific gene enrichment analysis

The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.

Last updated 2 months ago

genesetenrichmentgeneexpressionsequencing

5.93 score 57 scripts 431 downloads

INDEED - Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.

Last updated 2 months ago

immunooncologysoftwareresearchfieldbiologicalquestionstatisticalmethoddifferentialexpressionmassspectrometrymetabolomics

5.92 score 4 stars 10 scripts 116 downloads

FELLA - Interpretation and enrichment for metabolomics data

Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.

Last updated 2 months ago

softwaremetabolomicsgraphandnetworkkegggopathwaysnetworknetworkenrichment

5.90 score 25 scripts 282 downloads

PathoStat - PathoStat Statistical Microbiome Analysis Package

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.

Last updated 2 months ago

microbiomemetagenomicsgraphandnetworkmicroarraypatternlogicprincipalcomponentsequencingsoftwarevisualizationrnaseqimmunooncology

5.90 score 8 stars 7 scripts 372 downloads

rnaseqcomp - Benchmarks for RNA-seq Quantification Pipelines

Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation.

Last updated 2 months ago

rnaseqvisualizationqualitycontrol

5.90 score 8 stars 3 scripts 223 downloads

MetaNeighbor - Single cell replicability analysis

MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.

Last updated 2 months ago

immunooncologygeneexpressiongomultiplecomparisonsinglecelltranscriptomics

5.89 score 77 scripts 323 downloads

rexposome - Exposome exploration and outcome data analysis

Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.

Last updated 2 months ago

softwarebiologicalquestioninfrastructuredataimportdatarepresentationbiomedicalinformaticsexperimentaldesignmultiplecomparisonclassificationclustering

5.88 score 1 dependents 28 scripts 226 downloads

miRspongeR - Identification and analysis of miRNA sponge regulation

This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.

Last updated 2 months ago

geneexpressionbiomedicalinformaticsnetworkenrichmentsurvivalmicroarraysoftwaresinglecellspatialrnaseqcernamirnasponge

5.88 score 5 stars 8 scripts 93 downloads

regsplice - L1-regularization based methods for detection of differential splicing

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.

Last updated 2 months ago

immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicingsequencingrnaseqmicroarrayexonarrayexperimentaldesignsoftware

5.86 score 3 stars 27 scripts 171 downloads

epiNEM - epiNEM

epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways. It is tailored towards large scale double knock-out screens.

Last updated 2 months ago

pathwayssystemsbiologynetworkinferencenetwork

5.83 score 1 stars 3 dependents 1 scripts 257 downloads

cicero - Predict cis-co-accessibility from single-cell chromatin accessibility data

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.

Last updated 2 months ago

sequencingclusteringcellbasedassaysimmunooncologygeneregulationgenetargetepigeneticsatacseqsinglecell

5.80 score 314 scripts 541 downloads

CEMiTool - Co-expression Modules identification Tool

The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.

Last updated 2 months ago

geneexpressiontranscriptomicsgraphandnetworkmrnamicroarrayrnaseqnetworknetworkenrichmentpathwaysimmunooncology

5.79 score 41 scripts 320 downloads

twoddpcr - Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

The twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad's QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes 'definetherain' (Jones et al., 2014) and 'ddpcRquant' (Trypsteen et al., 2015) which both handle one channel ddPCR experiments only. The 'ddpcr' package available on CRAN (Attali et al., 2016) supports automatic gating of a specific class of two channel ddPCR experiments only.

Last updated 2 months ago

ddpcrsoftwareclassification

5.78 score 10 stars 4 scripts 210 downloads

TVTB - TVTB: The VCF Tool Box

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

Last updated 2 months ago

softwaregeneticsgeneticvariabilitygenomicvariationdatarepresentationguidnaseqwholegenomevisualizationmultiplecomparisondataimportvariantannotationsequencingcoveragealignmentsequencematching

5.76 score 2 stars 16 scripts 206 downloads

BPRMeth - Model higher-order methylation profiles

The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions or cells according to their methylation profiles.

Last updated 2 months ago

immunooncologydnamethylationgeneexpressiongeneregulationepigeneticsgeneticsclusteringfeatureextractionregressionrnaseqbayesiankeggsequencingcoveragesinglecellopenblascpp

5.75 score 1 dependents 94 scripts 242 downloads

miRSM - Inferring miRNA sponge modules in heterogeneous data

The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.

Last updated 2 months ago

geneexpressionbiomedicalinformaticsclusteringgenesetenrichmentmicroarraysoftwaregeneregulationgenetargetcernamirnamirna-spongemirna-targetsmodules

5.75 score 4 stars 5 scripts 152 downloads

stageR - stageR: stage-wise analysis of high throughput gene expression data in R

The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published in Genome Biology at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0

Last updated 2 months ago

softwarestatisticalmethod

5.71 score 86 scripts 501 downloads

GOfuncR - Gene ontology enrichment using FUNC

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph is included in the package and updated regularly (01-May-2021). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.

Last updated 2 months ago

genesetenrichmentgocpp

5.69 score 55 scripts 744 downloads

bigmelon - Illumina methylation array analysis for large experiments

Methods for working with Illumina arrays using gdsfmt.

Last updated 2 months ago

dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarraydataimportcpgisland

5.69 score 28 scripts 310 downloads

GDCRNATools - GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.

Last updated 2 months ago

immunooncologygeneexpressiondifferentialexpressiongeneregulationgenetargetnetworkinferencesurvivalvisualizationgenesetenrichmentnetworkenrichmentnetworkrnaseqgokegg

5.64 score 44 scripts 426 downloads

cydar - Using Mass Cytometry for Differential Abundance Analyses

Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

Last updated 2 months ago

immunooncologyflowcytometrymultiplecomparisonproteomicssinglecellcpp

5.64 score 48 scripts 217 downloads

statTarget - Statistical Analysis of Molecular Profiles

A streamlined tool provides a graphical user interface for quality control based signal drift correction (QC-RFSC), integration of data from multi-batch MS-based experiments, and the comprehensive statistical analysis in metabolomics and proteomics.

Last updated 2 months ago

immunooncologymetabolomicsproteomicsmachine learninglipidomicsmassspectrometryqualitycontrolnormalizationqc-rfsccombatdifferentialexpressionbatcheffectvisualizationmultiplecomparisonpreprocessingsoftware

5.64 score 24 scripts 241 downloads

breakpointR - Find breakpoints in Strand-seq data

This package implements functions for finding breakpoints, plotting and export of Strand-seq data.

Last updated 2 months ago

softwaresequencingdnaseqsinglecellcoverage

5.60 score 8 stars 10 scripts 301 downloads

DNAshapeR - High-throughput prediction of DNA shape features

DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.

Last updated 2 months ago

structuralpredictiondna3dstructuresoftwarecpp

5.58 score 38 scripts 216 downloads

synergyfinder - Calculate and Visualize Synergy Scores for Drug Combinations

Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.

Last updated 2 months ago

softwarestatisticalmethod

5.58 score 42 scripts 446 downloads

MetID - Network-based prioritization of putative metabolite IDs

This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.

Last updated 2 months ago

assaydomainbiologicalquestioninfrastructureresearchfieldstatisticalmethodtechnologyworkflowstepnetworkkegg

5.55 score 1 stars 71 scripts 156 downloads

wiggleplotr - Make read coverage plots from BigWig files

Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

Last updated 2 months ago

immunooncologycoveragernaseqchipseqsequencingvisualizationgeneexpressiontranscriptionalternativesplicing

5.49 score 1 dependents 26 scripts 398 downloads

cellbaseR - Querying annotation data from the high performance Cellbase web

This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

Last updated 2 months ago

annotationvariantannotation

5.48 score 2 stars 6 scripts 252 downloads

RIVER - R package for RIVER (RNA-Informed Variant Effect on Regulation)

An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.

Last updated 2 months ago

geneexpressiongeneticvariabilitysnptranscriptionfunctionalpredictiongeneregulationgenomicvariationbiomedicalinformaticsfunctionalgenomicsgeneticssystemsbiologytranscriptomicsbayesianclusteringtranscriptomevariantregressionfunctional-variantsvariant

5.48 score 10 stars 5 scripts 195 downloads

yamss - Tools for high-throughput metabolomics

Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis. At the core of these methods is a peak detection phase that pools information across all samples simultaneously. This is in contrast to other methods that detect peaks in a sample-by-sample basis.

Last updated 2 months ago

massspectrometrymetabolomicspeakdetectionsoftware

5.48 score 3 stars 9 scripts 284 downloads

Director - A dynamic visualization tool of multi-level data

Director is an R package designed to streamline the visualization of molecular effects in regulatory cascades. It utilizes the R package htmltools and a modified Sankey plugin of the JavaScript library D3 to provide a fast and easy, browser-enabled solution to discovering potentially interesting downstream effects of regulatory and/or co-expressed molecules. The diagrams are robust, interactive, and packaged as highly-portable HTML files that eliminate the need for third-party software to view. This enables a straightforward approach for scientists to interpret the data produced, and bioinformatics developers an alternative means to present relevant data.

Last updated 2 months ago

visualization

5.48 score 9 scripts 130 downloads

TCseq - Time course sequencing data analysis

Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.

Last updated 2 months ago

epigeneticstimecoursesequencingchipseqrnaseqdifferentialexpressionclusteringvisualization

5.45 score 28 scripts 520 downloads

maser - Mapping Alternative Splicing Events to pRoteins

This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.

Last updated 2 months ago

alternativesplicingtranscriptomicsvisualization

5.44 score 18 stars 17 scripts 379 downloads

GEM - GEM: fast association study for the interplay of Gene, Environment and Methylation

Tools for analyzing EWAS, methQTL and GxE genome widely.

Last updated 2 months ago

methylseqmethylationarraygenomewideassociationregressiondnamethylationsnpgeneexpressiongui

5.43 score 27 scripts 164 downloads

diffuStats - Diffusion scores on biological networks

Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels, which can derive from gene expression, genome-wide association studies, protein domains or metabolomics profiling, are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation, characterisation and benchmarking.

Last updated 2 months ago

networkgeneexpressiongraphandnetworkmetabolomicstranscriptomicsproteomicsgeneticsgenomewideassociationnormalizationcpp

5.40 score 42 scripts 201 downloads

RITAN - Rapid Integration of Term Annotation and Network resources

Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.

Last updated 2 months ago

qualitycontrolnetworknetworkenrichmentnetworkinferencegenesetenrichmentfunctionalgenomicsgraphandnetwork

5.40 score 9 scripts 242 downloads

Rbowtie2 - An R Wrapper for Bowtie2 and AdapterRemoval

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.

Last updated 2 months ago

sequencingalignmentpreprocessing

5.39 score 3 dependents 27 scripts 638 downloads

sevenC - Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.

Last updated 2 months ago

dna3dstructurechipchipcoveragedataimportepigeneticsfunctionalgenomicsclassificationregressionchipseqhicannotation3d-genomechip-seqchromatin-interactionhi-cpredictionsequence-motiftranscription-factors

5.38 score 12 stars 3 scripts 196 downloads

SeqSQC - A bioconductor package for sample quality check with next generation sequencing data

The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.

Last updated 2 months ago

experiment datahomo_sapiens_datasequencing dataproject1000genomesgenome

5.38 score 2 scripts 398 downloads

ASpli - Analysis of Alternative Splicing Using RNA-Seq

Integrative pipeline for the analysis of alternative splicing using RNAseq.

Last updated 2 months ago

immunooncologygeneexpressiontranscriptionalternativesplicingcoveragedifferentialexpressiondifferentialsplicingtimecoursernaseqgenomeannotationsequencingalignment

5.33 score 1 dependents 45 scripts 352 downloads

DaMiRseq - Data Mining for RNA-seq data: normalization, feature selection and classification

The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot.

Last updated 2 months ago

sequencingrnaseqclassificationimmunooncologyopenjdk

5.32 score 1 dependents 7 scripts 254 downloads

CNVPanelizer - Reliable CNV detection in targeted sequencing applications

A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.

Last updated 2 months ago

classificationsequencingnormalizationcopynumbervariationcoverage

5.32 score 12 scripts 246 downloads

SPLINTER - Splice Interpreter of Transcripts

Provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

Last updated 2 months ago

immunooncologygeneexpressionrnaseqvisualizationalternativesplicing

5.30 score 1 scripts 201 downloads

topdownr - Investigation of Fragmentation Conditions in Top-Down Proteomics

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

Last updated 2 months ago

immunooncologyinfrastructureproteomicsmassspectrometrycoveragemass-spectrometrytopdown

5.26 score 1 stars 220 downloads

SNPediaR - Query data from SNPedia

SNPediaR provides some tools for downloading and parsing data from the SNPedia web site <http://www.snpedia.com>. The implemented functions allow users to import the wiki text available in SNPedia pages and to extract the most relevant information out of them. If some information in the downloaded pages is not automatically processed by the library functions, users can easily implement their own parsers to access it in an efficient way.

Last updated 2 months ago

snpvariantannotation

5.26 score 9 stars 5 scripts 148 downloads

heatmaps - Flexible Heatmaps for Functional Genomics and Sequence Features

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

Last updated 2 months ago

visualizationsequencematchingfunctionalgenomics

5.23 score 1 dependents 19 scripts 378 downloads

omicsPrint - Cross omic genetic fingerprinting

omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).

Last updated 2 months ago

qualitycontrolgeneticsepigeneticstranscriptomicsdnamethylationtranscriptiongeneticvariabilityimmunooncology

5.20 score 32 scripts 213 downloads

runibic - runibic: row-based biclustering algorithm for analysis of gene expression data in R

This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.

Last updated 2 months ago

microarrayclusteringgeneexpressionsequencingcoveragecppopenmp

5.20 score 4 stars 7 scripts 206 downloads

biotmle - Targeted Learning with Moderated Statistics for Biomarker Discovery

Tools for differential expression biomarker discovery based on microarray and next-generation sequencing data that leverage efficient semiparametric estimators of the average treatment effect for variable importance analysis. Estimation and inference of the (marginal) average treatment effects of potential biomarkers are computed by targeted minimum loss-based estimation, with joint, stable inference constructed across all biomarkers using a generalization of moderated statistics for use with the estimated efficient influence function. The procedure accommodates the use of ensemble machine learning for the estimation of nuisance functions.

Last updated 2 months ago

regressiongeneexpressiondifferentialexpressionsequencingmicroarrayrnaseqimmunooncologybioconductorbioconductor-packagebioconductor-packagesbioinformaticsbiomarker-discoverybiostatisticscausal-inferencecomputational-biologymachine-learningstatisticstargeted-learning

5.20 score 4 stars 5 scripts 292 downloads

ASICS - Automatic Statistical Identification in Complex Spectra

With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) <doi:10.1007/s11306-017-1244-5>.

Last updated 2 months ago

softwaredataimportcheminformaticsmetabolomics

5.18 score 30 scripts 372 downloads

DMRScan - Detection of Differentially Methylated Regions

This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.

Last updated 2 months ago

softwaretechnologysequencingwholegenome

5.15 score 2 stars 3 scripts 179 downloads

rCGH - Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

Last updated 2 months ago

acghcopynumbervariationpreprocessingfeatureextraction

5.10 score 4 stars 1 dependents 26 scripts 268 downloads

icetea - Integrating Cap Enrichment with Transcript Expression Analysis

icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.

Last updated 2 months ago

immunooncologytranscriptiongeneexpressionsequencingrnaseqtranscriptomicsdifferentialexpressioncageexpressionrna-seq

5.08 score 2 stars 7 scripts 160 downloads

IMMAN - Interlog protein network reconstruction by Mapping and Mining ANalysis

Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable.

Last updated 2 months ago

sequencematchingalignmentsystemsbiologygraphandnetworknetworkproteomics

5.08 score 3 scripts 183 downloads

tRNAscanImport - Importing a tRNAscan-SE result file as GRanges object

The package imports the result of tRNAscan-SE as a GRanges object.

Last updated 2 months ago

softwaredataimportworkflowsteppreprocessingvisualizationbioconductorsequencesstructurestrnatrnascantrnascan-se

5.08 score 2 stars 3 scripts 228 downloads

semisup - Semi-Supervised Mixture Model

Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.

Last updated 2 months ago

snpgenomicvariationsomaticmutationgeneticsclassificationclusteringdnaseqmicroarraymultiplecomparison

5.08 score 1 stars 4 scripts 186 downloads

MetaboSignal - MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

Last updated 2 months ago

graphandnetworkgenesignalinggenetargetnetworkpathwayskeggreactomesoftware

5.08 score 6 scripts 314 downloads

epivizrData - Data Management API for epiviz interactive visualization app

Serve data from Bioconductor Objects through a WebSocket connection.

Last updated 2 months ago

infrastructurevisualization

5.08 score 1 stars 4 dependents 4 scripts 240 downloads

recoup - An R package for the creation of complex genomic profile plots

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

Last updated 2 months ago

immunooncologysoftwaregeneexpressionpreprocessingqualitycontrolrnaseqchipseqsequencingcoverageatacseqchiponchipalignmentdataimport

5.02 score 1 stars 2 scripts 205 downloads

SIMD - Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site

This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article 'Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data' by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).

Last updated 2 months ago

immunooncologydifferentialmethylationsinglecelldifferentialexpression

5.00 score 1 scripts 177 downloads

GARS - GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets

Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. Several methods have been proposed to perform feature selection: most of them relies on univariate statistics, correlation, entropy measurements or the usage of backward/forward regressions. Herein, we propose an efficient, robust and fast method that adopts stochastic optimization approaches for high-dimensional. GARS is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.

Last updated 2 months ago

classificationfeatureextractionclusteringopenjdk

5.00 score 2 scripts 189 downloads

coseq - Co-Expression Analysis of Sequencing Data

Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

Last updated 2 months ago

geneexpressionrnaseqsequencingsoftwareimmunooncology

4.98 score 16 scripts 337 downloads

yarn - YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

Last updated 2 months ago

softwarequalitycontrolgeneexpressionsequencingpreprocessingnormalizationannotationvisualizationclustering

4.97 score 1 dependents 31 scripts 340 downloads

Harman - The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.

Last updated 2 months ago

batcheffectmicroarraymultiplecomparisonprincipalcomponentnormalizationpreprocessingdnamethylationtranscriptionsoftwarestatisticalmethodcpp

4.97 score 1 dependents 31 scripts 312 downloads

RSeqAn - R SeqAn

Headers and some wrapper functions from the SeqAn C++ library for ease of usage in R.

Last updated 2 months ago

infrastructuresoftwarecpp

4.95 score 3 stars 1 dependents 2 scripts 240 downloads

RVS - Computes estimates of the probability of related individuals sharing a rare variant

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

Last updated 2 months ago

immunooncologygeneticsgenomewideassociationvariantdetectionexomeseqwholegenome

4.95 score 9 scripts 159 downloads

gcapc - GC Aware Peak Caller

Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

Last updated 2 months ago

sequencingchipseqbatcheffectpeakdetection

4.95 score 9 stars 7 scripts 186 downloads

sigFeature - sigFeature: Significant feature selection using SVM-RFE & t-statistic

This package provides a novel feature selection algorithm for binary classification using support vector machine recursive feature elimination SVM-RFE and t-statistic. In this feature selection process, the selected features are differentially significant between the two classes and also they are good classifier with higher degree of classification accuracy.

Last updated 2 months ago

featureextractiongeneexpressionmicroarraytranscriptionmrnamicroarraygenepredictionnormalizationclassificationsupportvectormachine

4.92 score 21 scripts 418 downloads

Oscope - Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.

Last updated 2 months ago

immunooncologystatisticalmethodrnaseqsequencinggeneexpression

4.92 score 1 dependents 14 scripts 334 downloads

EGAD - Extending guilt by association by degree

The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.

Last updated 2 months ago

softwarefunctionalgenomicssystemsbiologygenepredictionfunctionalpredictionnetworkenrichmentgraphandnetworknetwork

4.92 score 83 scripts 206 downloads

myvariant - Accesses MyVariant.info variant query and annotation services

MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services

Last updated 2 months ago

variantannotationannotationgenomicvariation

4.91 score 27 scripts 231 downloads

AnnotationHubData - Transform public data resources into Bioconductor Data Structures

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

Last updated 2 months ago

dataimport

4.90 score 3 dependents 22 scripts 814 downloads

mfa - Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

MFA models genomic bifurcations using a Bayesian hierarchical mixture of factor analysers.

Last updated 2 months ago

immunooncologyrnaseqgeneexpressionbayesiansinglecellcpp

4.85 score 35 scripts 283 downloads

IMAS - Integrative analysis of Multi-omics data for Alternative Splicing

Integrative analysis of Multi-omics data for Alternative splicing.

Last updated 2 months ago

immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressiongeneregulationregressionrnaseqsequencingsnpsoftwaretranscription

4.85 score 1 scripts 210 downloads

GRmetrics - Calculate growth-rate inhibition (GR) metrics

Functions for calculating and visualizing growth-rate inhibition (GR) metrics.

Last updated 2 months ago

immunooncologycellbasedassayscellbiologysoftwaretimecoursevisualization

4.83 score 1 stars 17 scripts 218 downloads

rhdf5client - Access HDF5 content from HDF Scalable Data Service

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

Last updated 2 months ago

dataimportsoftwareinfrastructure

4.82 score 2 dependents 37 scripts 286 downloads

transcriptogramer - Transcriptional analysis based on transcriptograms

R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.

Last updated 2 months ago

softwarenetworkvisualizationsystemsbiologygeneexpressiongenesetenrichmentgraphandnetworkclusteringdifferentialexpressionmicroarrayrnaseqtranscriptionimmunooncology

4.81 score 4 stars 9 scripts 228 downloads

plotGrouper - Shiny app GUI wrapper for ggplot with built-in statistical analysis

A shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).

Last updated 2 months ago

immunooncologyflowcytometrygraphandnetworkstatisticalmethoddataimportguimultiplecomparisonbioconductorggplot2plottingshiny

4.78 score 6 stars 10 scripts 136 downloads

SCBN - A statistical normalization method and differential expression analysis for RNA-seq data between different species

This package provides a scale based normalization (SCBN) method to identify genes with differential expression between different species. It takes into account the available knowledge of conserved orthologous genes and the hypothesis testing framework to detect differentially expressed orthologous genes. The method on this package are described in the article 'A statistical normalization method and differential expression analysis for RNA-seq data between different species' by Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin, Jun Zhang (2018, pending publication).

Last updated 2 months ago

differentialexpressiongeneexpressionnormalization

4.78 score 1 dependents 1 scripts 190 downloads

FitHiC - Confidence estimation for intra-chromosomal contact maps

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Last updated 2 months ago

dna3dstructuresoftwarecpp

4.78 score 2 scripts 303 downloads

gCrisprTools - Suite of Functions for Pooled Crispr Screen QC and Analysis

Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.

Last updated 2 months ago

immunooncologycrisprpooledscreensexperimentaldesignbiomedicalinformaticscellbiologyfunctionalgenomicspharmacogenomicspharmacogeneticssystemsbiologydifferentialexpressiongenesetenrichmentgeneticsmultiplecomparisonnormalizationpreprocessingqualitycontrolrnaseqregressionsoftwarevisualization

4.78 score 8 scripts 202 downloads

ClusterSignificance - The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. ClusterSignificance accomplishes this by, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.

Last updated 2 months ago

clusteringclassificationprincipalcomponentstatisticalmethod

4.78 score 4 scripts 187 downloads

Sconify - A toolkit for performing KNN-based statistics for flow and mass cytometry data

This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps"fold change" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold.

Last updated 2 months ago

immunooncologysinglecellflowcytometrysoftwaremultiplecomparisonvisualization

4.74 score 11 scripts 197 downloads

openPrimeR - Multiplex PCR Primer Design and Analysis

An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package.

Last updated 2 months ago

softwaretechnologycoveragemultiplecomparison

4.74 score 22 scripts 286 downloads

MetaCyto - MetaCyto: A package for meta-analysis of cytometry data

This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.

Last updated 2 months ago

immunooncologycellbiologyflowcytometryclusteringstatisticalmethodsoftwarecellbasedassayspreprocessing

4.73 score 18 scripts 213 downloads

miRLAB - Dry lab for exploring miRNA-mRNA relationships

Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.

Last updated 2 months ago

mirnageneexpressionnetworkinferencenetwork

4.72 score 11 scripts 231 downloads

consensus - Cross-platform consensus analysis of genomic measurements via interlaboratory testing method

An implementation of the American Society for Testing and Materials (ASTM) Standard E691 for interlaboratory testing procedures, designed for cross-platform genomic measurements. Given three (3) or more genomic platforms or laboratory protocols, this package provides interlaboratory testing procedures giving per-locus comparisons for sensitivity and precision between platforms.

Last updated 2 months ago

qualitycontrolregressiondatarepresentationgeneexpressionmicroarrayrnaseq

4.70 score 10 scripts 158 downloads

strandCheckR - Calculate strandness information of a bam file

This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.

Last updated 2 months ago

rnaseqalignmentqualitycontrolcoverageimmunooncology

4.70 score 7 scripts 213 downloads

scmeth - Functions to conduct quality control analysis in methylation data

Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.

Last updated 2 months ago

dnamethylationqualitycontrolpreprocessingsinglecellimmunooncologybioconductor-packagemethylationsingle-cell-methylation

4.70 score 5 scripts 226 downloads

epivizrChart - R interface to epiviz web components

This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer.

Last updated 2 months ago

visualizationgui

4.68 score 12 scripts 205 downloads

Anaquin - Statistical analysis of sequins

The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.

Last updated 2 months ago

immunooncologydifferentialexpressionpreprocessingrnaseqgeneexpressionsoftware

4.65 score 45 scripts 278 downloads

phenopath - Genomic trajectories with heterogeneous genetic and environmental backgrounds

PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them.

Last updated 2 months ago

immunooncologyrnaseqgeneexpressionbayesiansinglecellprincipalcomponentcpp

4.63 score 43 scripts 228 downloads

iasva - Iteratively Adjusted Surrogate Variable Analysis

Iteratively Adjusted Surrogate Variable Analysis (IA-SVA) is a statistical framework to uncover hidden sources of variation even when these sources are correlated. IA-SVA provides a flexible methodology to i) identify a hidden factor for unwanted heterogeneity while adjusting for all known factors; ii) test the significance of the putative hidden factor for explaining the unmodeled variation in the data; and iii), if significant, use the estimated factor as an additional known factor in the next iteration to uncover further hidden factors.

Last updated 2 months ago

preprocessingqualitycontrolbatcheffectrnaseqsoftwarestatisticalmethodfeatureextractionimmunooncology

4.62 score 42 scripts 186 downloads

mdp - Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes.

Last updated 2 months ago

biomedicalinformaticsqualitycontroltranscriptomicssystemsbiologymicroarray

4.62 score 14 scripts 160 downloads

branchpointer - Prediction of intronic splicing branchpoints

Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.

Last updated 2 months ago

softwaregenomeannotationgenomicvariationmotifannotation

4.62 score 21 scripts 236 downloads

geneClassifiers - Application of gene classifiers

This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.

Last updated 2 months ago

geneexpressionbiomedicalinformaticsclassificationsurvivalmicroarray

4.62 score 1 stars 35 scripts 183 downloads

ddPCRclust - Clustering algorithm for ddPCR data

The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.

Last updated 2 months ago

ddpcrclusteringbiological-data-analysis

4.60 score 4 stars 4 scripts 208 downloads

methInheritSim - Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.

Last updated 2 months ago

biologicalquestionepigeneticsdnamethylationdifferentialmethylationmethylseqsoftwareimmunooncologystatisticalmethodwholegenomesequencingbisulphite-sequencinginheritancemethylationsimulation

4.60 score 1 stars 1 scripts 236 downloads

GA4GHshiny - Shiny application for interacting with GA4GH-based data servers

GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.

Last updated 2 months ago

gui

4.60 score 2 stars 3 scripts 217 downloads

methylInheritance - Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

Last updated 2 months ago

biologicalquestionepigeneticsdnamethylationdifferentialmethylationmethylseqsoftwareimmunooncologystatisticalmethodwholegenomesequencinganalysisbioconductorbioinformaticscpgdifferentially-methylated-elementsinheritancemonte-carlo-samplingpermutation

4.60 score 1 scripts 194 downloads

IsoCorrectoR - Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments

IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as ultra-high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR. NOTE: With R version 4.0.0, writing correction results to Excel files may currently not work on Windows. However, writing results to csv works as before.

Last updated 2 months ago

softwaremetabolomicsmassspectrometrypreprocessingimmunooncology

4.56 score 1 dependents 7 scripts 188 downloads

Pigengene - Infers biological signatures from gene expression data

Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.

Last updated 2 months ago

geneexpressionrnaseqnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdecisiontreedimensionreductionprincipalcomponentmicroarraynormalizationimmunooncology

4.56 score 1 dependents 10 scripts 242 downloads

INSPEcT - Modeling RNA synthesis, processing and degradation with RNA-seq data

INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data.

Last updated 2 months ago

sequencingrnaseqgeneregulationtimecoursesystemsbiology

4.56 score 9 scripts 388 downloads

ChIPComp - Quantitative comparison of multiple ChIP-seq datasets

ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.

Last updated 2 months ago

chipseqsequencingtranscriptiongeneticscoveragemultiplecomparisondataimport

4.49 score 51 scripts 324 downloads

ERSSA - Empirical RNA-seq Sample Size Analysis

The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate levels. This allows the user to determine, without relying on any a priori assumptions, whether sufficient differential detection has been acheived with their RNA-seq dataset.

Last updated 2 months ago

immunooncologygeneexpressiontranscriptiondifferentialexpressionrnaseqmultiplecomparisonqualitycontrol

4.48 score 1 scripts 207 downloads

primirTSS - Prediction of pri-miRNA Transcription Start Site

A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

Last updated 2 months ago

immunooncologysequencingrnaseqgeneticspreprocessingtranscriptiongeneregulation

4.48 score 2 scripts 168 downloads

gep2pep - Creation and Analysis of Pathway Expression Profiles (PEPs)

Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.

Last updated 2 months ago

geneexpressiondifferentialexpressiongenesetenrichmentdimensionreductionpathwaysgo

4.48 score 4 scripts 193 downloads

ANF - Affinity Network Fusion for Complex Patient Clustering

This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion.

Last updated 2 months ago

clusteringgraphandnetworknetwork

4.48 score 9 scripts 344 downloads

omicRexposome - Exposome and omic data associatin and integration analysis

omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

Last updated 2 months ago

immunooncologyworkflowstepmultiplecomparisonvisualizationgeneexpressiondifferentialexpressiondifferentialmethylationgeneregulationepigeneticsproteomicstranscriptomicsstatisticalmethodregression

4.48 score 5 scripts 203 downloads

MSstatsQC - Longitudinal system suitability monitoring and quality control for proteomic experiments

MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.

Last updated 2 months ago

softwarequalitycontrolproteomicsmassspectrometry

4.48 score 1 dependents 7 scripts 199 downloads

msgbsR - msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Pipeline for the anaysis of a MS-GBS experiment.

Last updated 2 months ago

immunooncologydifferentialmethylationdataimportepigeneticsmethylseq

4.48 score 1 scripts 209 downloads

PPInfer - Inferring functionally related proteins using protein interaction networks

Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.

Last updated 2 months ago

softwarestatisticalmethodnetworkgraphandnetworkgenesetenrichmentnetworkenrichmentpathways

4.48 score 1 dependents 4 scripts 440 downloads

flowTime - Annotation and analysis of biological dynamical systems using flow cytometry

This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.

Last updated 2 months ago

flowcytometrytimecoursevisualizationdataimportcellbasedassaysimmunooncology

4.48 score 8 scripts 222 downloads

GA4GHclient - A Bioconductor package for accessing GA4GH API data servers

GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

Last updated 2 months ago

datarepresentationthirdpartyclient

4.48 score 1 stars 1 dependents 3 scripts 250 downloads

BiocSklearn - interface to python sklearn via Rstudio reticulate

This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.

Last updated 2 months ago

statisticalmethoddimensionreductioninfrastructure

4.44 score 11 scripts 273 downloads

clusterSeq - Clustering of high-throughput sequencing data by identifying co-expression patterns

Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.

Last updated 2 months ago

sequencingdifferentialexpressionmultiplecomparisonclusteringgeneexpression

4.38 score 2 scripts 223 downloads

pqsfinder - Identification of potential quadruplex forming sequences

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

Last updated 2 months ago

motifdiscoverysequencematchinggeneregulationcpp

4.38 score 15 scripts 278 downloads

ChIPanalyser - ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.

Last updated 2 months ago

softwarebiologicalquestionworkflowsteptranscriptionsequencingchiponchipcoveragealignmentchipseqsequencematchingdataimportpeakdetection

4.34 score 11 scripts 244 downloads

scoreInvHap - Get inversion status in predefined regions

scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.

Last updated 2 months ago

snpgeneticsgenomicvariation

4.34 score 11 scripts 204 downloads

GeneStructureTools - Tools for spliced gene structure manipulation and analysis

GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.

Last updated 2 months ago

immunooncologysoftwaredifferentialsplicingfunctionalpredictiontranscriptomicsalternativesplicingrnaseq

4.32 score 21 scripts 260 downloads

basecallQC - Working with Illumina Basecalling and Demultiplexing input and output files

The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.

Last updated 2 months ago

sequencinginfrastructuredataimportqualitycontrol

4.32 score 21 scripts 214 downloads

XINA - Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

The aim of XINA is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. XINA imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. XINA, not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs.

Last updated 2 months ago

systemsbiologyproteomicsrnaseqnetwork

4.30 score 3 scripts 248 downloads

Ularcirc - Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.

Last updated 2 months ago

datarepresentationvisualizationgeneticssequencingannotationcoveragealternativesplicingdifferentialsplicing

4.30 score 4 scripts 189 downloads

GIGSEA - Genotype Imputed Gene Set Enrichment Analysis

We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal.

Last updated 2 months ago

genesetenrichmentsnpvariantannotationgeneexpressiongeneregulationregressiondifferentialexpression

4.30 score 2 scripts 127 downloads

InTAD - Search for correlation between epigenetic signals and gene expression in TADs

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.

Last updated 2 months ago

epigeneticssequencingchipseqrnaseqhicgeneexpressionimmunooncology

4.30 score 7 scripts 196 downloads

iCNV - Integrated Copy Number Variation detection

Integrative copy number variation (CNV) detection from multiple platform and experimental design.

Last updated 2 months ago

immunooncologyexomeseqwholegenomesnpcopynumbervariationhiddenmarkovmodel

4.30 score 5 scripts 211 downloads

scFeatureFilter - A correlation-based method for quality filtering of single-cell RNAseq data

An R implementation of the correlation-based method developed in the Joshi laboratory to analyse and filter processed single-cell RNAseq data. It returns a filtered version of the data containing only genes expression values unaffected by systematic noise.

Last updated 2 months ago

immunooncologysinglecellrnaseqpreprocessinggeneexpression

4.30 score 20 scripts 184 downloads

loci2path - Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.

Last updated 2 months ago

functionalgenomicsgeneticsgenesetenrichmentsoftwaregeneexpressionsequencingcoveragebiocarta

4.30 score 1 stars 2 scripts 236 downloads

OPWeight - Optimal p-value weighting with independent information

This package perform weighted-pvalue based multiple hypothesis test and provides corresponding information such as ranking probability, weight, significant tests, etc . To conduct this testing procedure, the testing method apply a probabilistic relationship between the test rank and the corresponding test effect size.

Last updated 2 months ago

immunooncologybiomedicalinformaticsmultiplecomparisonregressionrnaseqsnp

4.30 score 2 stars 184 downloads

motifcounter - R package for analysing TFBSs in DNA sequences

'motifcounter' provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher-order background models and accounting for self-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higher-order nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self-overlapping motif structures as exemplified by repeat-like or palindromic motifs, and allow to determine the p-value and fold-enrichment for a set of observed motif matches.

Last updated 2 months ago

transcriptionmotifannotationsequencematchingsoftwareopenmp

4.30 score 7 scripts 197 downloads

rqt - rqt: utilities for gene-level meta-analysis

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

Last updated 2 months ago

genomewideassociationregressionsurvivalprincipalcomponentstatisticalmethodsequencing

4.30 score 2 stars 4 scripts 150 downloads

cellscape - Explores single cell copy number profiles in the context of a single cell tree

CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.

Last updated 2 months ago

visualization

4.30 score 5 scripts 168 downloads

goSTAG - A tool to use GO Subtrees to Tag and Annotate Genes within a set

Gene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and thousands of genes systematically is impractical by manually curating the annotation and function of each gene. Over-representation analysis (ORA) of genes was developed to identify biological themes. Given a Gene Ontology (GO) and an annotation of genes that indicate the categories each one fits into, significance of the over-representation of the genes within the ontological categories is determined by a Fisher's exact test or modeling according to a hypergeometric distribution. Comparing a small number of enriched biological categories for a few samples is manageable using Venn diagrams or other means for assessing overlaps. However, with hundreds of enriched categories and many samples, the comparisons are laborious. Furthermore, if there are enriched categories that are shared between samples, trying to represent a common theme across them is highly subjective. goSTAG uses GO subtrees to tag and annotate genes within a set. goSTAG visualizes the similarities between the over-representation of DEGs by clustering the p-values from the enrichment statistical tests and labels clusters with the GO term that has the most paths to the root within the subtree generated from all the GO terms in the cluster.

Last updated 2 months ago

geneexpressiondifferentialexpressiongenesetenrichmentclusteringmicroarraymrnamicroarrayrnaseqvisualizationgoimmunooncology

4.30 score 1 scripts 210 downloads

ChIPexoQual - ChIPexoQual

Package with a quality control pipeline for ChIP-exo/nexus data.

Last updated 2 months ago

chipseqsequencingtranscriptionvisualizationqualitycontrolcoveragealignment

4.30 score 1 stars 5 scripts 329 downloads

RJMCMCNucleosomes - Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

Last updated 2 months ago

biologicalquestionchipseqnucleosomepositioningsoftwarestatisticalmethodbayesiansequencingcoveragebayesian-t-mixturebioconductorc-plus-plusgenome-wide-profilingmultinomial-dirichlet-priornucleosome-positioningnucleosomesreversible-jump-mcmcgslcpp

4.30 score 1 scripts 210 downloads

BiocWorkflowTools - Tools to aid the development of Bioconductor Workflow packages

Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.

Last updated 2 months ago

softwarereportwriting

4.30 score 10 scripts 456 downloads

GeneGeneInteR - Tools for Testing Gene-Gene Interaction at the Gene Level

The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results. <doi:10.18637/jss.v095.i12>.

Last updated 2 months ago

genomewideassociationsnpgeneticsgeneticvariabilitycpp

4.30 score 2 scripts 177 downloads

NanoStringDiff - Differential Expression Analysis of NanoString nCounter Data

This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.

Last updated 2 months ago

differentialexpressionnormalizationcpp

4.30 score 3 scripts 227 downloads

IONiseR - Quality Assessment Tools for Oxford Nanopore MinION data

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

Last updated 2 months ago

qualitycontroldataimportsequencing

4.30 score 5 scripts 338 downloads

anota2seq - Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

anota2seq provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source (i.e. translated mRNA or total mRNA). Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels (i.e. changes in translated mRNA that are independent of levels of total mRNA) or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels (i.e. changes in total mRNA that are independent of levels of translated mRNA). anota2seq applies analysis of partial variance and the random variance model to fulfill these tasks.

Last updated 2 months ago

immunooncologygeneexpressiondifferentialexpressionmicroarraygenomewideassociationbatcheffectnormalizationrnaseqsequencinggeneregulationregression

4.28 score 12 scripts 402 downloads

LedPred - Learning from DNA to Predict Enhancers

This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.

Last updated 2 months ago

supportvectormachinesoftwaremotifannotationchipseqsequencingclassification

4.26 score 3 stars 3 scripts 154 downloads

ivygapSE - A SummarizedExperiment for Ivy-GAP data

Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.

Last updated 2 months ago

transcriptionsoftwarevisualizationsurvivalgeneexpressionsequencing

4.20 score 16 scripts 190 downloads

HelloRanges - Introduce *Ranges to bedtools users

Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

Last updated 2 months ago

sequencingannotationcoveragegenomeannotationdataimportsequencematchingvariantannotation

4.19 score 1 dependents 26 scripts 268 downloads

BLMA - BLMA: A package for bi-level meta-analysis

Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.

Last updated 2 months ago

genesetenrichmentpathwaysdifferentialexpressionmicroarray

4.18 score 51 scripts 240 downloads

pogos - PharmacOGenomics Ontology Support

Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.

Last updated 2 months ago

pharmacogenomicspooledscreensimmunooncology

4.18 score 8 scripts 195 downloads

tenXplore - ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics

Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.

Last updated 2 months ago

immunooncologydimensionreductionprincipalcomponenttranscriptomicssinglecell

4.18 score 7 scripts 176 downloads

bnbc - Bandwise normalization and batch correction of Hi-C data

Tools to normalize (several) Hi-C data from replicates.

Last updated 2 months ago

hicpreprocessingnormalizationsoftwarecpp

4.18 score 1 stars 15 scripts 438 downloads

MCbiclust - Massive correlating biclusters for gene expression data and associated methods

Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

Last updated 2 months ago

immunooncologyclusteringmicroarraystatisticalmethodsoftwarernaseqgeneexpression

4.18 score 2 scripts 228 downloads

odseq - Outlier detection in multiple sequence alignments

Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for aligned sequences and a variant using string kernels for unaligned sequences.

Last updated 2 months ago

alignmentmultiplesequencealignment

4.18 score 1 dependents 25 scripts 170 downloads

BUMHMM - Computational pipeline for computing probability of modification from structure probing experiment data

This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.

Last updated 2 months ago

immunooncologygeneticvariabilitytranscriptiongeneexpressiongeneregulationcoveragegeneticsstructuralpredictiontranscriptomicsbayesianclassificationfeatureextractionhiddenmarkovmodelregressionrnaseqsequencing

4.15 score 14 scripts 232 downloads

DeMAND - DeMAND

DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.

Last updated 2 months ago

systemsbiologynetworkenrichmentgeneexpressionstatisticalmethodnetwork

4.15 score 9 scripts 180 downloads

geneplast - Evolutionary and plasticity analysis of orthologous groups

Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.

Last updated 2 months ago

geneticsgeneregulationsystemsbiology

4.13 score 17 scripts 242 downloads

hmdbQuery - utilities for exploration of human metabolome database

Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).

Last updated 2 months ago

metabolomicsinfrastructure

4.11 score 13 scripts 216 downloads

methimpute - Imputation-guided re-construction of complete methylomes from WGBS data

This package implements functions for calling methylation for all cytosines in the genome.

Last updated 2 months ago

immunooncologysoftwarednamethylationepigeneticshiddenmarkovmodelsequencingcoveragecppopenmp

4.11 score 13 scripts 212 downloads

qPLEXanalyzer - Tools for quantitative proteomics data analysis

Tools for TMT based quantitative proteomics data analysis.

Last updated 2 months ago

immunooncologyproteomicsmassspectrometrynormalizationpreprocessingqualitycontroldataimport

4.08 score 1 stars 9 scripts 187 downloads

slalom - Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors. The method uses Bayesian factor analysis with a latent variable model to identify active pathways (selected by the user, e.g. KEGG pathways) that explain variation in a single-cell RNA-seq dataset. This an R/C++ implementation of the f-scLVM Python package. See the publication describing the method at https://doi.org/10.1186/s13059-017-1334-8.

Last updated 2 months ago

immunooncologysinglecellrnaseqnormalizationvisualizationdimensionreductiontranscriptomicsgeneexpressionsequencingsoftwarereactomekeggopenblascpp

4.08 score 12 scripts 349 downloads

panelcn.mops - CNV detection tool for targeted NGS panel data

CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.

Last updated 2 months ago

sequencingcopynumbervariationcellbiologygenomicvariationvariantdetectiongenetics

4.08 score 12 scripts 245 downloads

banocc - Bayesian ANalysis Of Compositional Covariance

BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element.

Last updated 2 months ago

immunooncologymetagenomicssoftwarebayesian

4.08 score 12 scripts 318 downloads

CINdex - Chromosome Instability Index

The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.

Last updated 2 months ago

softwarecopynumbervariationgenomicvariationacghmicroarraygeneticssequencing

4.08 score 2 scripts 196 downloads

AffiXcan - A Functional Approach To Impute Genetically Regulated Expression

Impute a GReX (Genetically Regulated Expression) for a set of genes in a sample of individuals, using a method based on the Total Binding Affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known.

Last updated 2 months ago

geneexpressiontranscriptiongeneregulationdimensionreductionregressionprincipalcomponent

4.00 score 328 downloads

OMICsPCA - An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it's core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals.

Last updated 2 months ago

immunooncologymultiplecomparisonprincipalcomponentdatarepresentationworkflowvisualizationdimensionreductionclusteringbiologicalquestionepigeneticsworkflowtranscriptiongeneticvariabilityguibiomedicalinformaticsepigeneticsfunctionalgenomicssinglecell

4.00 score 1 scripts 195 downloads

BUScorrect - Batch Effects Correction with Unknown Subtypes

High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity.

Last updated 2 months ago

geneexpressionstatisticalmethodbayesianclusteringfeatureextractionbatcheffect

4.00 score 2 scripts 172 downloads

nuCpos - An R package for prediction of nucleosome positions

nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.

Last updated 2 months ago

geneticsepigeneticsnucleosomepositioning

4.00 score 1 scripts 142 downloads

celaref - Single-cell RNAseq cell cluster labelling by reference

After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).

Last updated 2 months ago

singlecell

4.00 score 5 scripts 182 downloads

hierinf - Hierarchical Inference

Tools to perform hierarchical inference for one or multiple studies / data sets based on high-dimensional multivariate (generalised) linear models. A possible application is to perform hierarchical inference for GWA studies to find significant groups or single SNPs (if the signal is strong) in a data-driven and automated procedure. The method is based on an efficient hierarchical multiple testing correction and controls the FWER. The functions can easily be run in parallel.

Last updated 2 months ago

clusteringgenomewideassociationlinkagedisequilibriumregressionsnp

4.00 score 2 scripts 122 downloads

CellTrails - Reconstruction, visualization and analysis of branching trajectories

CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.

Last updated 2 months ago

immunooncologyclusteringdatarepresentationdifferentialexpressiondimensionreductiongeneexpressionsequencingsinglecellsoftwaretimecourse

4.00 score 7 scripts 162 downloads

GMRP - GWAS-based Mendelian Randomization and Path Analyses

Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease.

Last updated 2 months ago

sequencingregressionsnp

4.00 score 3 scripts 200 downloads

FastqCleaner - A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.

Last updated 2 months ago

qualitycontrolsequencingsoftwaresangerseqsequencematchingcpp

4.00 score 4 scripts 198 downloads

MBttest - Multiple Beta t-Tests

MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.

Last updated 2 months ago

sequencingdifferentialexpressionmultiplecomparisonsagegeneexpressiontranscriptionalternativesplicingcoveragedifferentialsplicing

4.00 score 3 scripts 178 downloads

MSstatsQCgui - A graphical user interface for MSstatsQC package

MSstatsQCgui is a Shiny app which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.

Last updated 2 months ago

softwarequalitycontrolproteomicsmassspectrometrygui

4.00 score 1 scripts 166 downloads

ccfindR - Cancer Clone Finder

A collection of tools for cancer genomic data clustering analyses, including those for single cell RNA-seq. Cell clustering and feature gene selection analysis employ Bayesian (and maximum likelihood) non-negative matrix factorization (NMF) algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations. Analysis outputs are factor matrices for multiple ranks and marginal likelihood values for each rank. The package includes utilities for downstream analyses, including meta-gene identification, visualization, and construction of rank-based trees for clusters.

Last updated 2 months ago

transcriptomicssinglecellimmunooncologybayesianclusteringgslcpp

4.00 score 10 scripts 238 downloads

CytoDx - Robust prediction of clinical outcomes using cytometry data without cell gating

This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.

Last updated 2 months ago

immunooncologycellbiologyflowcytometrystatisticalmethodsoftwarecellbasedassaysregressionclassificationsurvival

4.00 score 8 scripts 255 downloads

CellScore - Tool for Evaluation of Cell Identity from Transcription Profiles

The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.

Last updated 2 months ago

geneexpressiontranscriptionmicroarraymultiplecomparisonreportwritingdataimportvisualization

4.00 score 5 scripts 196 downloads

powerTCR - Model-Based Comparative Analysis of the TCR Repertoire

This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.

Last updated 2 months ago

softwareclusteringbiomedicalinformatics

4.00 score 4 scripts 671 downloads

TTMap - Two-Tier Mapper: a clustering tool based on topological data analysis

TTMap is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free.

Last updated 2 months ago

softwaremicroarraydifferentialexpressionmultiplecomparisonclusteringclassification

4.00 score 214 downloads

omicplotR - Visual Exploration of Omic Datasets Using a Shiny App

A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata.

Last updated 2 months ago

softwaredifferentialexpressiongeneexpressionguirnaseqdnaseqmetagenomicstranscriptomicsbayesianmicrobiomevisualizationsequencingimmunooncology

4.00 score 5 scripts 188 downloads

gsean - Gene Set Enrichment Analysis with Networks

Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.

Last updated 2 months ago

softwarestatisticalmethodnetworkgraphandnetworkgenesetenrichmentgeneexpressionnetworkenrichmentpathwaysdifferentialexpression

4.00 score 1 scripts 198 downloads

BiFET - Bias-free Footprint Enrichment Test

BiFET identifies TFs whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias. For this, we use the number of target regions with footprints for TF k, t_k as a test statistic and calculate the p-value as the probability of observing t_k or more target regions with footprints under the null hypothesis.

Last updated 2 months ago

immunooncologygeneticsepigeneticstranscriptiongeneregulationatacseqdnaseseqripseqsoftware

4.00 score 5 scripts 307 downloads

seqCAT - High Throughput Sequencing Cell Authentication Toolkit

The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.

Last updated 2 months ago

coveragegenomicvariationsequencingvariantannotation

4.00 score 216 downloads

TFARM - Transcription Factors Association Rules Miner

It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules.

Last updated 2 months ago

biologicalquestioninfrastructurestatisticalmethodtranscription

4.00 score 2 scripts 202 downloads

TFHAZ - Transcription Factor High Accumulation Zones

It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.

Last updated 2 months ago

softwarebiologicalquestiontranscriptionchipseqcoverage

4.00 score 2 scripts 200 downloads

Doscheda - A DownStream Chemo-Proteomics Analysis Pipeline

Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.

Last updated 2 months ago

proteomicsnormalizationpreprocessingmassspectrometryqualitycontroldataimportregression

4.00 score 2 scripts 204 downloads

pgca - PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data

Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.

Last updated 2 months ago

workflowstepassaydomainproteomicsmassspectrometryimmunooncology

4.00 score 3 scripts 154 downloads

NADfinder - Call wide peaks for sequencing data

Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation.

Last updated 2 months ago

sequencingdnaseqgeneregulationpeakdetection

4.00 score 1 scripts 218 downloads

timescape - Patient Clonal Timescapes

TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.

Last updated 2 months ago

visualizationbiomedicalinformatics

4.00 score 7 scripts 206 downloads

mapscape - mapscape

MapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each sample. The output of MapScape consists of a cropped anatomical image surrounded by two representations of each tumour sample. The first, a cellular aggregate, visually displays the prevalence of each clone. The second shows a skeleton of the clonal phylogeny while highlighting only those clones present in the sample. Together, these representations enable the analyst to visualize the distribution of clones throughout anatomic space.

Last updated 2 months ago

visualization

4.00 score 5 scripts 134 downloads

fCCAC - functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomics, as it allows both to evaluate reproducibility of replicates, and to compare different datasets to identify potential correlations. fCCAC applies functional Canonical Correlation Analysis to allow the assessment of: (i) reproducibility of biological or technical replicates, analyzing their shared covariance in higher order components; and (ii) the associations between different datasets. fCCAC represents a more sophisticated approach that complements Pearson correlation of genomic coverage.

Last updated 2 months ago

epigeneticstranscriptionsequencingcoveragechipseqfunctionalgenomicsrnaseqatacseqmnaseseq

4.00 score 1 scripts 192 downloads

KEGGlincs - Visualize all edges within a KEGG pathway and overlay LINCS data

See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

Last updated 2 months ago

networkinferencegeneexpressiondatarepresentationthirdpartyclientcellbiologygraphandnetworkpathwayskeggnetwork

4.00 score 3 scripts 220 downloads

BaalChIP - BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.

Last updated 2 months ago

softwarechipseqbayesiansequencing

4.00 score 5 scripts 300 downloads

geneAttribution - Identification of candidate genes associated with genetic variation

Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.

Last updated 2 months ago

snpgenepredictiongenomewideassociationvariantannotationgenomicvariation

4.00 score 3 scripts 203 downloads

GAprediction - Prediction of gestational age with Illumina HumanMethylation450 data

[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data.

Last updated 2 months ago

immunooncologydnamethylationepigeneticsregressionbiomedicalinformatics

4.00 score 167 downloads

ctsGE - Clustering of Time Series Gene Expression data

Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.

Last updated 2 months ago

immunooncologygeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentgeneticsbayesianclusteringtimecoursesequencingrnaseq

4.00 score 1 stars 3 scripts 188 downloads

ccmap - Combination Connectivity Mapping

Finds drugs and drug combinations that are predicted to reverse or mimic gene expression signatures. These drugs might reverse diseases or mimic healthy lifestyles.

Last updated 2 months ago

geneexpressiontranscriptionmicroarraydifferentialexpression

4.00 score 5 scripts 208 downloads

sights - Statistics and dIagnostic Graphs for HTS

SIGHTS is a suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity.

Last updated 2 months ago

immunooncologycellbasedassaysmicrotitreplateassaynormalizationmultiplecomparisonpreprocessingqualitycontrolbatcheffectvisualization

4.00 score 9 scripts 160 downloads

netprioR - A model for network-based prioritisation of genes

A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.

Last updated 2 months ago

immunooncologycellbasedassayspreprocessingnetwork

4.00 score 1 scripts 152 downloads

covRNA - Multivariate Analysis of Transcriptomic Data

This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.

Last updated 2 months ago

geneexpressiontranscription

4.00 score 1 scripts 186 downloads

LymphoSeq - Analyze high-throughput sequencing of T and B cell receptors

This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.

Last updated 2 months ago

softwaretechnologysequencingtargetedresequencingalignmentmultiplesequencealignment

4.00 score 4 scripts 214 downloads

IntEREst - Intron-Exon Retention Estimator

This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

Last updated 2 months ago

softwarealternativesplicingcoveragedifferentialsplicingsequencingrnaseqalignmentnormalizationdifferentialexpressionimmunooncology

3.98 score 12 scripts 238 downloads

CellMapper - Predict genes expressed selectively in specific cell types

Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before.

Last updated 2 months ago

microarraysoftwaregeneexpression

3.95 score 15 scripts 182 downloads

geneXtendeR - Optimized Functional Annotation Of ChIP-seq Data

geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

Last updated 2 months ago

chipseqgeneticsannotationgenomeannotationdifferentialpeakcallingcoveragepeakdetectionchiponchiphistonemodificationdataimportnaturallanguageprocessingvisualizationgosoftwarebioconductorbioinformaticscchip-seqcomputational-biologyepigeneticsfunctional-annotation

3.95 score 9 stars 5 scripts 274 downloads

CONFESS - Cell OrderiNg by FluorEScence Signal

Single Cell Fluidigm Spot Detector.

Last updated 2 months ago

immunooncologygeneexpressiondataimportcellbiologyclusteringrnaseqqualitycontrolvisualizationtimecourseregressionclassification

3.90 score 2 scripts 225 downloads

RareVariantVis - A suite for analysis of rare genomic variants in whole genome sequencing data

Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.

Last updated 2 months ago

genomicvariationsequencingwholegenome

3.90 score 1 scripts 224 downloads

CHRONOS - CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.

Last updated 2 months ago

systemsbiologygraphandnetworkpathwayskeggopenjdk

3.82 score 11 scripts 213 downloads

oncomix - Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data

This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes.

Last updated 2 months ago

geneexpressionsequencing

3.78 score 4 scripts 179 downloads

cbaf - Automated functions for comparing various omic data from cbioportal.org

This package contains functions that allow analysing and comparing omic data across various cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.

Last updated 2 months ago

softwareassaydomaindnamethylationgeneexpressiontranscriptionmicroarrayresearchfieldbiomedicalinformaticscomparativegenomicsepigeneticsgeneticstranscriptomics

3.78 score 1 scripts 208 downloads

DMCHMM - Differentially Methylated CpG using Hidden Markov Model

A pipeline for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data. DNA methylation studies have enabled researchers to understand methylation patterns and their regulatory roles in biological processes and disease. However, only a limited number of statistical approaches have been developed to provide formal quantitative analysis. Specifically, a few available methods do identify differentially methylated CpG (DMC) sites or regions (DMR), but they suffer from limitations that arise mostly due to challenges inherent in bisulfite sequencing data. These challenges include: (1) that read-depths vary considerably among genomic positions and are often low; (2) both methylation and autocorrelation patterns change as regions change; and (3) CpG sites are distributed unevenly. Furthermore, there are several methodological limitations: almost none of these tools is capable of comparing multiple groups and/or working with missing values, and only a few allow continuous or multiple covariates. The last of these is of great interest among researchers, as the goal is often to find which regions of the genome are associated with several exposures and traits. To tackle these issues, we have developed an efficient DMC identification method based on Hidden Markov Models (HMMs) called “DMCHMM” which is a three-step approach (model selection, prediction, testing) aiming to address the aforementioned drawbacks.

Last updated 2 months ago

differentialmethylationsequencinghiddenmarkovmodelcoverage

3.78 score 3 scripts 192 downloads

RTNduals - Analysis of co-regulation and inference of 'dual regulons'

RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer 'dual regulons', a new concept that tests whether regulators can co-operate or compete in influencing targets.

Last updated 2 months ago

generegulationgeneexpressionnetworkenrichmentnetworkinferencegraphandnetwork

3.78 score 1 dependents 2 scripts 254 downloads

MWASTools - MWASTools: an integrated pipeline to perform metabolome-wide association studies

MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.

Last updated 2 months ago

metabolomicslipidomicscheminformaticssystemsbiologyqualitycontrol

3.78 score 1 dependents 3 scripts 312 downloads

DEsubs - DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.

Last updated 2 months ago

systemsbiologygraphandnetworkpathwayskegggeneexpressionnetworkenrichmentnetworkrnaseqdifferentialexpressionnormalizationimmunooncology

3.78 score 1 scripts 192 downloads

AMOUNTAIN - Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. AMOUNTAIN aims to search active modules in multi-layer WGCN using a continuous optimization approach.

Last updated 2 months ago

geneexpressionmicroarraydifferentialexpressionnetworkgsl

3.78 score 1 dependents 1 scripts 299 downloads

MGFR - Marker Gene Finder in RNA-seq data

The package is designed to detect marker genes from RNA-seq data.

Last updated 2 months ago

immunooncologygeneticsgeneexpressionrnaseq

3.78 score 1 dependents 2 scripts 202 downloads

iGC - An integrated analysis package of Gene expression and Copy number alteration

This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

Last updated 2 months ago

softwarebiological questiondifferentialexpressiongenomicvariationassaydomaincopynumbervariationgeneexpressionresearchfieldgeneticstechnologymicroarraysequencingworkflowstepmultiplecomparison

3.78 score 1 stars 1 scripts 208 downloads

funtooNorm - Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.

Last updated 2 months ago

dnamethylationpreprocessingnormalization

3.70 score 204 downloads

mimager - mimager: The Microarray Imager

Easily visualize and inspect microarrays for spatial artifacts.

Last updated 2 months ago

infrastructurevisualizationmicroarraybioconductorbioinformatics

3.70 score 3 scripts 226 downloads

hipathia - HiPathia: High-throughput Pathway Analysis

Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.

Last updated 2 months ago

pathwaysgraphandnetworkgeneexpressiongenesignalinggo

3.62 score 42 scripts 426 downloads

SDAMS - Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

This Package utilizes a Semi-parametric Differential Abundance/expression analysis (SDA) method for metabolomics and proteomics data from mass spectrometry as well as single-cell RNA sequencing data. SDA is able to robustly handle non-normally distributed data and provides a clear quantification of the effect size.

Last updated 2 months ago

immunooncologydifferentialexpressionmetabolomicsproteomicsmassspectrometrysinglecell

3.60 score 1 scripts 192 downloads

TMixClust - Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.

Last updated 2 months ago

softwarestatisticalmethodclusteringtimecoursegeneexpression

3.60 score 5 scripts 233 downloads

phosphonormalizer - Compensates for the bias introduced by median normalization in

It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

Last updated 2 months ago

softwarestatisticalmethodworkflowstepnormalizationproteomics

3.60 score 2 scripts 152 downloads

GOpro - Find the most characteristic gene ontology terms for groups of human genes

Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).

Last updated 2 months ago

annotationclusteringgogeneexpressiongenesetenrichmentmultiplecomparisoncpp

3.60 score 2 stars 4 scripts 298 downloads

ASAFE - Ancestry Specific Allele Frequency Estimation

Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.

Last updated 2 months ago

snpgenomewideassociationlinkagedisequilibriumbiomedicalinformaticsgeneticsexperimentaldesign

3.60 score 2 scripts 284 downloads

esetVis - Visualizations of expressionSet Bioconductor object

Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.

Last updated 2 months ago

visualizationdatarepresentationdimensionreductionprincipalcomponentpathways

3.60 score 6 scripts 205 downloads

MADSEQ - Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.

Last updated 2 months ago

genomicvariationsomaticmutationvariantdetectionbayesiancopynumbervariationsequencingcoveragejagscpp

3.60 score 4 stars 1 scripts 189 downloads

eudysbiome - Cartesian plot and contingency test on 16S Microbial data

eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.

Last updated 2 months ago

3.60 score 2 scripts 200 downloads

CausalR - Causal network analysis methods

Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.

Last updated 2 months ago

immunooncologysystemsbiologynetworkgraphandnetworknetwork inferencetranscriptomicsproteomicsdifferentialexpressionrnaseqmicroarray

3.60 score 7 scripts 176 downloads

LRBaseDbi - DBI to construct LRBase-related package

Interface to construct LRBase package (LRBase.XXX.eg.db).

Last updated 2 months ago

infrastructure

3.48 score 1 scripts 228 downloads

appreci8R - appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.

Last updated 2 months ago

variantdetectiongeneticvariabilitysnpvariantannotationsequencing

3.48 score 1 scripts 184 downloads

DominoEffect - Identification and Annotation of Protein Hotspot Residues

The functions support identification and annotation of hotspot residues in proteins. These are individual amino acids that accumulate mutations at a much higher rate than their surrounding regions.

Last updated 2 months ago

softwaresomaticmutationproteomicssequencematchingalignment

3.48 score 1 scripts 194 downloads

TFEA.ChIP - Analyze Transcription Factor Enrichment

Package to analize transcription factor enrichment in a gene set using data from ChIP-Seq experiments.

Last updated 2 months ago

transcriptiongeneregulationgenesetenrichmenttranscriptomicssequencingchipseqrnaseqimmunooncology

3.48 score 15 scripts 230 downloads

vulcan - VirtUaL ChIP-Seq data Analysis using Networks

Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.

Last updated 2 months ago

systemsbiologynetworkenrichmentgeneexpressionchipseq

3.38 score 12 scripts 238 downloads

ExCluster - ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition

ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.

Last updated 2 months ago

immunooncologydifferentialsplicingrnaseqsoftware

3.30 score 1 scripts 144 downloads

sparsenetgls - Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

The package provides methods of combining the graph structure learning and generalized least squares regression to improve the regression estimation. The main function sparsenetgls() provides solutions for multivariate regression with Gaussian distributed dependant variables and explanatory variables utlizing multiple well-known graph structure learning approaches to estimating the precision matrix, and uses a penalized variance covariance matrix with a distance tuning parameter of the graph structure in deriving the sandwich estimators in generalized least squares (gls) regression. This package also provides functions for assessing a Gaussian graphical model which uses the penalized approach. It uses Receiver Operative Characteristics curve as a visualization tool in the assessment.

Last updated 2 months ago

immunooncologygraphandnetworkregressionmetabolomicscopynumbervariationmassspectrometryproteomicssoftwarevisualization

3.30 score 3 scripts 152 downloads

ipdDb - IPD IMGT/HLA and IPD KIR database for Homo sapiens

All alleles from the IPD IMGT/HLA <https://www.ebi.ac.uk/ipd/imgt/hla/> and IPD KIR <https://www.ebi.ac.uk/ipd/kir/> database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.

Last updated 2 months ago

genomicvariationsequencematchingvariantannotationdatarepresentationannotationhubsoftware

3.30 score 4 scripts 380 downloads

Rmmquant - RNA-Seq multi-mapping Reads Quantification Tool

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.

Last updated 2 months ago

geneexpressiontranscriptionzlibcpp

3.30 score 5 scripts 216 downloads

missRows - Handling Missing Individuals in Multi-Omics Data Integration

The missRows package implements the MI-MFA method to deal with missing individuals ('biological units') in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are combined in a single consensus solution. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.

Last updated 2 months ago

softwarestatisticalmethoddimensionreductionprincipalcomponentmathematicalbiologyvisualization

3.30 score 3 scripts 180 downloads

GateFinder - Projection-based Gating Strategy Optimization for Flow and Mass Cytometry

Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.

Last updated 2 months ago

immunooncologyflowcytometrycellbiologyclustering

3.30 score 7 scripts 202 downloads

DEScan2 - Differential Enrichment Scan 2

Integrated peak and differential caller, specifically designed for broad epigenomic signals.

Last updated 2 months ago

immunooncologypeakdetectionepigeneticssoftwaresequencingcoveragecpp

3.30 score 2 scripts 207 downloads

ClusterJudge - Judging Quality of Clustering Methods using Mutual Information

ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.

Last updated 2 months ago

softwarestatisticalmethodclusteringgeneexpressiongo

3.30 score 3 scripts 213 downloads

RTNsurvival - Survival analysis using transcriptional networks inferred by the RTN package

RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user's specifications.

Last updated 2 months ago

networkenrichmentsurvivalgeneregulationgenesetenrichmentnetworkinferencegraphandnetwork

3.30 score 9 scripts 197 downloads

Scale4C - Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

Scale4C is an R/Bioconductor package for scale-space transformation and visualization of 4C-seq data. The scale-space transformation is a multi-scale visualization technique to transform a 2D signal (e.g. 4C-seq reads on a genomic interval of choice) into a tesselation in the scale space (2D, genomic position x scale factor) by applying different smoothing kernels (Gauss, with increasing sigma). This transformation allows for explorative analysis and comparisons of the data's structure with other samples.

Last updated 2 months ago

visualizationqualitycontroldataimportsequencingcoverage

3.30 score 1 scripts 230 downloads

IWTomics - Interval-Wise Testing for Omics Data

Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.

Last updated 2 months ago

statisticalmethodmultiplecomparisondifferentialexpressiondifferentialmethylationdifferentialpeakcallinggenomeannotationdataimport

3.30 score 5 scripts 246 downloads

CCPROMISE - PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.

Last updated 2 months ago

microarraygeneexpression

3.30 score 1 scripts 197 downloads

uSORT - uSORT: A self-refining ordering pipeline for gene selection

This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.

Last updated 2 months ago

immunooncologyrnaseqguicellbiologydnaseq

3.30 score 222 downloads

BayesKnockdown - BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. Can also be used for differential expression/2-class data.

Last updated 2 months ago

networkinferencegeneexpressiongenetargetnetworkbayesian

3.30 score 1 scripts 260 downloads

MODA - MODA: MOdule Differential Analysis for weighted gene co-expression network

MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.

Last updated 2 months ago

geneexpressionmicroarraydifferentialexpressionnetwork

3.30 score 9 scripts 185 downloads

qsea - IP-seq data analysis and vizualization

qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.

Last updated 2 months ago

sequencingdnamethylationcpgislandchipseqpreprocessingnormalizationqualitycontrolvisualizationcopynumbervariationchiponchipdifferentialmethylation

3.30 score 7 scripts 192 downloads

covEB - Empirical Bayes estimate of block diagonal covariance matrices

Using bayesian methods to estimate correlation matrices assuming that they can be written and estimated as block diagonal matrices. These block diagonal matrices are determined using shrinkage parameters that values below this parameter to zero.

Last updated 2 months ago

immunooncologybayesianmicroarrayrnaseqpreprocessingsoftwaregeneexpressionstatisticalmethod

3.30 score 2 scripts 176 downloads

epivizrStandalone - Run Epiviz Interactive Genomic Data Visualization App within R

This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The 'epivizrServer' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.

Last updated 2 months ago

visualizationinfrastructuregui

3.30 score 3 scripts 196 downloads

MMDiff2 - Statistical Testing for ChIP-Seq data sets

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

Last updated 2 months ago

chipseqdifferentialpeakcallingsequencingsoftware

3.30 score 194 downloads

oppar - Outlier profile and pathway analysis in R

The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.

Last updated 2 months ago

pathwaysgenesetenrichmentsystemsbiologygeneexpressionsoftware

3.30 score 3 scripts 194 downloads

BadRegionFinder - BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

Last updated 2 months ago

coveragesequencingalignmentwholegenomeclassification

3.30 score 1 scripts 266 downloads

EBSEA - Exon Based Strategy for Expression Analysis of genes

Calculates differential expression of genes based on exon counts of genes obtained from RNA-seq sequencing data.

Last updated 2 months ago

softwaredifferentialexpressiongeneexpressionsequencing

3.30 score 4 scripts 172 downloads

ldblock - data structures for linkage disequilibrium measures in populations

Define data structures for linkage disequilibrium measures in populations.

Last updated 2 months ago

3.30 score 10 scripts 386 downloads

Path2PPI - Prediction of pathway-related protein-protein interaction networks

Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

Last updated 2 months ago

networkinferencesystemsbiologynetworkproteomicspathways

3.30 score 1 scripts 206 downloads

BBCAnalyzer - BBCAnalyzer: an R/Bioconductor package for visualizing base counts

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

Last updated 2 months ago

sequencingalignmentcoveragegeneticvariabilitysnp

3.30 score 1 scripts 319 downloads

synlet - Hits Selection for Synthetic Lethal RNAi Screen Data

Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.

Last updated 2 months ago

immunooncologycellbasedassaysqualitycontrolpreprocessingvisualizationfeatureextraction

3.30 score 2 scripts 191 downloads

traseR - GWAS trait-associated SNP enrichment analyses in genomic intervals

traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.

Last updated 2 months ago

geneticssequencingcoveragealignmentqualitycontroldataimport

3.30 score 3 scripts 218 downloads

fCI - f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.

Last updated 2 months ago

proteomics

3.30 score 5 scripts 203 downloads

MDTS - Detection of de novo deletion in targeted sequencing trios

A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.

Last updated 2 months ago

statisticalmethodtechnologysequencingtargetedresequencingcoveragedataimport

2.78 score 1 scripts 186 downloads

sscu - Strength of Selected Codon Usage

The package calculates the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp's method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) The package can detect the strength of translational accuracy selection by Akashi's test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi's test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function low_frequency_op in the package. The function try to find the low frequency optimal codons, among all the optimal codons identified by the op_highly function.

Last updated 2 months ago

geneticsgeneexpressionwholegenome

2.30 score 1 scripts 162 downloads

ISoLDE - Integrative Statistics of alleLe Dependent Expression

This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.

Last updated 2 months ago

immunooncologygeneexpressiontranscriptiongenesetenrichmentgeneticssequencingrnaseqmultiplecomparisonsnpgeneticvariabilityepigeneticsmathematicalbiologygeneregulationopenmp

2.30 score 2 scripts 140 downloads

dada2 - Accurate, high-resolution sample inference from amplicon sequencing data

The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

Last updated 2 months ago

immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioconductorbioinformaticsmetabarcodingtaxonomycpp

13.06 score 473 stars 4 dependents 2.2k scripts 4.8k downloads

tximport - Import and summarize transcript-level estimates for transcript- and gene-level analysis

Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

Last updated 2 months ago

dataimportpreprocessingrnaseqtranscriptomicstranscriptiongeneexpressionimmunooncologybioconductordeseq2

12.95 score 136 stars 11 dependents 2.5k scripts 5.2k downloads

ExperimentHub - Client to access ExperimentHub resources

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

Last updated 2 months ago

infrastructuredataimportguithirdpartyclientcore-package

12.13 score 9 stars 58 dependents 728 scripts 11k downloads

ggcyto - Visualize Cytometry data with ggplot

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.

Last updated 2 months ago

immunooncologyflowcytometrycellbasedassaysinfrastructurevisualization

11.39 score 56 stars 5 dependents 356 scripts 1.5k downloads

biomformat - An interface package for the BIOM file format

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

Last updated 2 months ago

immunooncologydataimportmetagenomicsmicrobiome

11.33 score 7 stars 39 dependents 376 scripts 8.7k downloads

scater - Single-Cell Analysis Toolkit for Gene Expression Data in R

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

Last updated 2 months ago

immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationvisualizationdimensionreductiontranscriptomicsgeneexpressionsequencingsoftwaredataimportdatarepresentationinfrastructurecoverage

11.05 score 40 dependents 12k scripts 12k downloads

EnrichedHeatmap - Making Enriched Heatmaps

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.

Last updated 2 months ago

softwarevisualizationsequencinggenomeannotationcoveragecpp

10.83 score 188 stars 1 dependents 328 scripts 1.0k downloads

SC3 - Single-Cell Consensus Clustering

A tool for unsupervised clustering and analysis of single cell RNA-Seq data.

Last updated 2 months ago

immunooncologysinglecellsoftwareclassificationclusteringdimensionreductionsupportvectormachinernaseqvisualizationtranscriptomicsdatarepresentationguidifferentialexpressiontranscriptionbioconductor-packagehuman-cell-atlassingle-cell-rna-seqopenblascpp

10.08 score 119 stars 1 dependents 370 scripts 608 downloads

GenVisR - Genomic Visualizations in R

Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.

Last updated 2 months ago

infrastructuredatarepresentationclassificationdnaseq

9.85 score 212 stars 79 scripts 511 downloads

biobroom - Turn Bioconductor objects into tidy data frames

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

Last updated 2 months ago

multiplecomparisondifferentialexpressionregressiongeneexpressionproteomicsdataimport

8.23 score 48 stars 1 dependents 292 scripts 470 downloads

BioQC - Detect tissue heterogeneity in expression profiles with gene sets

BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.

Last updated 2 months ago

geneexpressionqualitycontrolstatisticalmethodgenesetenrichmentcpp

8.15 score 5 stars 85 scripts 392 downloads

scde - Single Cell Differential Expression

The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).

Last updated 2 months ago

immunooncologyrnaseqstatisticalmethoddifferentialexpressionbayesiantranscriptionsoftwareanalysisbioinformaticsheterogenityngssingle-celltranscriptomicsopenblascppopenmp

7.71 score 173 stars 141 scripts 720 downloads

IHW - Independent Hypothesis Weighting

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.

Last updated 2 months ago

immunooncologymultiplecomparisonrnaseq

7.22 score 2 dependents 248 scripts 1.4k downloads

doppelgangR - Identify likely duplicate samples from genomic or meta-data

The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).

Last updated 2 months ago

immunooncologyrnaseqmicroarraygeneexpressionqualitycontrolbioconductor-package

6.67 score 5 stars 31 scripts 412 downloads

DiffLogo - DiffLogo: A comparative visualisation of biooligomer motifs

DiffLogo is an easy-to-use tool to visualize motif differences.

Last updated 2 months ago

softwaresequencematchingmultiplecomparisonmotifannotationvisualizationalignment

6.66 score 8 stars 27 scripts 208 downloads

Prostar - Provides a GUI for DAPAR

This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required.

Last updated 2 months ago

proteomicsmassspectrometrynormalizationpreprocessingsoftwareguiprostar1

6.65 score 1 stars 15 scripts 240 downloads

dupRadar - Assessment of duplication rates in RNA-Seq datasets

Duplication rate quality control for RNA-Seq datasets.

Last updated 2 months ago

technologysequencingrnaseqqualitycontrolimmunooncology

6.48 score 1 stars 60 scripts 310 downloads

SWATH2stats - Transform and Filter SWATH Data for Statistical Packages

This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

Last updated 2 months ago

proteomicsannotationexperimentaldesignpreprocessingmassspectrometryimmunooncology

6.47 score 1 stars 22 scripts 218 downloads

lpsymphony - Symphony integer linear programming solver in R

This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.

Last updated 2 months ago

infrastructurethirdpartyclientcoinor-symphony

6.46 score 3 dependents 16 scripts 1.9k downloads

subSeq - Subsampling of high-throughput sequencing count data

Subsampling of high throughput sequencing count data for use in experiment design and analysis.

Last updated 2 months ago

immunooncologysequencingtranscriptionrnaseqgeneexpressiondifferentialexpression

6.36 score 19 stars 20 scripts 222 downloads

ROTS - Reproducibility-Optimized Test Statistic

Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.

Last updated 2 months ago

softwaregeneexpressiondifferentialexpressionmicroarrayrnaseqproteomicsimmunooncologycpp

6.19 score 3 dependents 86 scripts 470 downloads

DAPAR - Tools for the Differential Analysis of Proteins Abundance with R

The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).

Last updated 2 months ago

proteomicsnormalizationpreprocessingmassspectrometryqualitycontrolgodataimportprostar1

5.66 score 2 stars 1 dependents 22 scripts 326 downloads

EmpiricalBrownsMethod - Uses Brown's method to combine p-values from dependent tests

Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.

Last updated 2 months ago

statisticalmethodgeneexpressionpathways

5.65 score 25 stars 3 dependents 7 scripts 262 downloads

flowAI - Automatic and interactive quality control for flow cytometry data

The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.

Last updated 2 months ago

flowcytometryqualitycontrolbiomedicalinformaticsimmunooncology

5.64 score 3 dependents 80 scripts 974 downloads

CrispRVariants - Tools for counting and visualising mutations in a target location

CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.

Last updated 2 months ago

immunooncologycrisprgenomicvariationvariantdetectiongeneticvariabilitydatarepresentationvisualizationsequencing

5.51 score 32 scripts 258 downloads

consensusSeekeR - Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions.

Last updated 2 months ago

biologicalquestionchipseqgeneticsmultiplecomparisontranscriptionpeakdetectionsequencingcoveragechip-seq-analysisgenomic-data-analysisnucleosome-positioning

5.43 score 1 stars 1 dependents 5 scripts 220 downloads

R4RNA - An R package for RNA visualization and analysis

A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.

Last updated 2 months ago

alignmentmultiplesequencealignmentpreprocessingvisualizationdataimportdatarepresentationmultiplecomparison

5.37 score 4 dependents 19 scripts 1.0k downloads

globalSeq - Global Test for Counts

The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size. Useful for testing for association between RNA-Seq and high-dimensional data.

Last updated 2 months ago

geneexpressionexonarraydifferentialexpressiongenomewideassociationtranscriptomicsdimensionreductionregressionsequencingwholegenomernaseqexomeseqmirnamultiplecomparison

5.32 score 1 stars 4 scripts 176 downloads

FamAgg - Pedigree Analysis and Familial Aggregation

Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.

Last updated 2 months ago

geneticspedigree

5.26 score 1 stars 5 scripts 206 downloads

Guitar - Guitar

The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

Last updated 2 months ago

sequencingsplicedalignmentalignmentdataimportrnaseqmethylseqqualitycontroltranscription

5.26 score 36 scripts 416 downloads

bacon - Controlling bias and inflation in association studies using the empirical null distribution

Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.

Last updated 2 months ago

immunooncologystatisticalmethodbayesianregressiongenomewideassociationtranscriptomicsrnaseqmethylationarraybatcheffectmultiplecomparison

5.18 score 95 scripts 401 downloads

nucleoSim - Generate synthetic nucleosome maps

This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.

Last updated 2 months ago

geneticssequencingsoftwarestatisticalmethodalignmentbioconductornucleosome-mapsnucleosomessimulationsimulatorsynthetic-nucleosomes

5.18 score 2 stars 8 scripts 184 downloads

MEAL - Perform methylation analysis

Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.

Last updated 2 months ago

dnamethylationmicroarraysoftwarewholegenome

4.98 score 24 scripts 239 downloads

iCARE - Individualized Coherent Absolute Risk Estimation (iCARE)

An R package to build, validate and apply absolute risk models

Last updated 2 months ago

softwarestatisticalmethodgenomewideassociation

4.78 score 9 scripts 323 downloads

Chicago - CHiCAGO: Capture Hi-C Analysis of Genomic Organization

A pipeline for analysing Capture Hi-C data.

Last updated 2 months ago

epigeneticshicsequencingsoftware

4.78 score 30 scripts 321 downloads

GeneBreak - Gene Break Detection

Recurrent breakpoint gene detection on copy number aberration profiles.

Last updated 2 months ago

acghcopynumbervariationdnaseqgeneticssequencingwholegenomevisualization

4.60 score 2 stars 6 scripts 204 downloads

chromPlot - Global visualization tool of genomic data

Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.

Last updated 2 months ago

datarepresentationfunctionalgenomicsgeneticssequencingannotationvisualization

4.53 score 24 scripts 446 downloads

ExpressionAtlas - Download datasets from EMBL-EBI Expression Atlas

This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.

Last updated 2 months ago

expressiondataexperimentdatasequencingdatamicroarraydataarrayexpress

4.45 score 20 scripts 478 downloads

GUIDEseq - GUIDE-seq and PEtag-seq analysis pipeline

The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.

Last updated 2 months ago

immunooncologygeneregulationsequencingworkflowstepcrispr

4.45 score 14 scripts 256 downloads

multiClust - multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles

Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.

Last updated 2 months ago

featureextractionclusteringgeneexpressionsurvival

4.34 score 11 scripts 202 downloads

RImmPort - RImmPort: Enabling Ready-for-analysis Immunology Research Data

The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.

Last updated 2 months ago

biomedicalinformaticsdataimportdatarepresentation

4.33 score 27 scripts 145 downloads

Uniquorn - Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

'Uniquorn' enables users to identify cancer cell lines. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file).

Last updated 2 months ago

immunooncologystatisticalmethodwholegenomeexomeseq

4.30 score 190 downloads

Mergeomics - Integrative network analysis of omics data

The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).

Last updated 2 months ago

software

4.30 score 8 scripts 184 downloads

RiboProfiling - Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

Last updated 2 months ago

riboseqsequencingcoveragealignmentqualitycontrolsoftwareprincipalcomponent

4.30 score 8 scripts 371 downloads

SMITE - Significance-based Modules Integrating the Transcriptome and Epigenome

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

Last updated 2 months ago

immunooncologydifferentialmethylationdifferentialexpressionsystemsbiologynetworkenrichmentgenomeannotationnetworksequencingrnaseqcoverage

4.26 score 1 stars 13 scripts 176 downloads

metaCCA - Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis

metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.

Last updated 2 months ago

genomewideassociationsnpgeneticsregressionstatisticalmethodsoftware

4.26 score 5 scripts 204 downloads

PCAN - Phenotype Consensus ANalysis (PCAN)

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

Last updated 2 months ago

annotationsequencinggeneticsfunctionalpredictionvariantannotationpathwaysnetwork

4.15 score 7 scripts 186 downloads

splineTimeR - Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.

Last updated 2 months ago

geneexpressiondifferentialexpressiontimecourseregressiongenesetenrichmentnetworkenrichmentnetworkinferencegraphandnetwork

4.01 score 17 scripts 210 downloads

biosigner - Signature discovery from omics data

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics.

Last updated 2 months ago

classificationfeatureextractiontranscriptomicsproteomicsmetabolomicslipidomicsmassspectrometry

4.00 score 10 scripts 356 downloads

MethPed - A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).

Last updated 2 months ago

immunooncologydnamethylationclassificationepigenetics

4.00 score 1 scripts 190 downloads

cellity - Quality Control for Single-Cell RNA-seq Data

A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets.

Last updated 2 months ago

immunooncologyrnaseqqualitycontrolpreprocessingnormalizationvisualizationdimensionreductiontranscriptomicsgeneexpressionsequencingsoftwaresupportvectormachine

4.00 score 9 scripts 202 downloads

GSALightning - Fast Permutation-based Gene Set Analysis

GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.

Last updated 2 months ago

softwarebiologicalquestiongenesetenrichmentdifferentialexpressiongeneexpressiontranscription

4.00 score 5 stars 4 scripts 148 downloads

QuaternaryProd - Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs

QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher's exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.

Last updated 2 months ago

graphandnetworkgeneexpressiontranscriptioncpp

4.00 score 1 scripts 182 downloads

SNPhood - SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

To date, thousands of single nucleotide polymorphisms (SNPs) have been found to be associated with complex traits and diseases. However, the vast majority of these disease-associated SNPs lie in the non-coding part of the genome, and are likely to affect regulatory elements, such as enhancers and promoters, rather than function of a protein. Thus, to understand the molecular mechanisms underlying genetic traits and diseases, it becomes increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin environment or transcription factor (TF) binding. Towards this aim, we developed SNPhood, a user-friendly *Bioconductor* R package to investigate and visualize the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region, perform various data quality checks, normalize read counts using additional input files, and to cluster and visualize the regions according to the binding pattern. The regions around each SNP can be binned in a user-defined fashion to allow for analysis of very broad patterns as well as a detailed investigation of specific binding shapes. Furthermore, SNPhood supports the integration with genotype information to investigate and visualize genotype-specific binding patterns. Finally, SNPhood can be employed for determining, investigating, and visualizing allele-specific binding patterns around the SNPs of interest.

Last updated 2 months ago

software

3.90 score 1 scripts 208 downloads

miRNAmeConverter - Convert miRNA Names to Different miRBase Versions

Translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/).

Last updated 2 months ago

preprocessingmirna

3.78 score 4 scripts 184 downloads

ExperimentHubData - Add resources to ExperimentHub

Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.

Last updated 2 months ago

infrastructuredataimportguithirdpartyclient

3.78 score 1 dependents 6 scripts 624 downloads

garfield - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

GARFIELD is a non-parametric functional enrichment analysis approach described in the paper GARFIELD: GWAS analysis of regulatory or functional information enrichment with LD correction. Briefly, it is a method that leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. It performs greedy pruning of GWAS SNPs (LD r2 > 0.1) and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and number of LD proxies (r2 > 0.8).

Last updated 2 months ago

softwarestatisticalmethodannotationfunctionalpredictiongenomeannotationcpp

3.30 score 6 scripts 172 downloads

BasicSTARRseq - Basic peak calling on STARR-seq data

Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.

Last updated 2 months ago

peakdetectiongeneregulationfunctionalpredictionfunctionalgenomicscoverage

3.30 score 1 scripts 277 downloads

RGraph2js - Convert a Graph into a D3js Script

Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.

Last updated 2 months ago

visualizationnetworkgraphandnetworkthirdpartyclient

3.30 score 1 scripts 184 downloads

transcriptR - An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events. Furthermore, the integration of ChIP- and RNA-seq data allows the identification all known and novel active transcription start sites within a given sample.

Last updated 2 months ago

immunooncologytranscriptionsoftwaresequencingrnaseqcoverage

3.30 score 2 scripts 300 downloads

profileScoreDist - Profile score distributions

Regularization and score distributions for position count matrices.

Last updated 2 months ago

softwaregeneregulationstatisticalmethodcpp

3.30 score 1 scripts 182 downloads

normalize450K - Preprocessing of Illumina Infinium 450K data

Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.

Last updated 2 months ago

normalizationdnamethylationmicroarraytwochannelpreprocessingmethylationarray

3.30 score 1 scripts 184 downloads

miRcomp - Tools to assess and compare miRNA expression estimatation methods

Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.

Last updated 2 months ago

softwareqpcrpreprocessingqualitycontrol

3.30 score 1 scripts 242 downloads

SICtools - Find SNV/Indel differences between two bam files with near relationship

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

Last updated 2 months ago

alignmentsequencingcoveragesequencematchingqualitycontroldataimportsoftwaresnpvariantdetection

3.30 score 1 scripts 291 downloads

iCheck - QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.

Last updated 2 months ago

geneexpressiondifferentialexpressionmicroarraypreprocessingdnamethylationonechanneltwochannelqualitycontrol

3.00 score 1 scripts 216 downloads

clustComp - Clustering Comparison Package

clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.

Last updated 2 months ago

geneexpressionclusteringvisualization

2.60 score 1 scripts 195 downloads

dcGSA - Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles

Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The dcGSA package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes.

Last updated 2 months ago

immunooncologygenesetenrichmentmicroarraystatisticalmethodsequencingrnaseqgeneexpression

2.30 score 1 scripts 185 downloads

ComplexHeatmap - Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Last updated 2 months ago

softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap

16.88 score 1.3k stars 147 dependents 14k scripts 25k downloads

AnnotationHub - Client to access AnnotationHub resources

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

Last updated 2 months ago

infrastructuredataimportguithirdpartyclientcore-package

14.01 score 17 stars 104 dependents 2.8k scripts 18k downloads

ChIPseeker - ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Last updated 2 months ago

annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics

13.04 score 229 stars 5 dependents 1.5k scripts 3.3k downloads

RUVSeq - Remove Unwanted Variation from RNA-Seq Data

This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

Last updated 2 months ago

immunooncologydifferentialexpressionpreprocessingrnaseqsoftware

9.87 score 12 stars 5 dependents 486 scripts 1.4k downloads

DEGreport - Report of DEG analysis

Creation of ready-to-share figures of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

Last updated 2 months ago

differentialexpressionvisualizationrnaseqreportwritinggeneexpressionimmunooncologybioconductordifferential-expressionqcreportrna-seqsmallrna

9.54 score 24 stars 1 dependents 347 scripts 1.1k downloads

monocle - Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

Last updated 2 months ago

immunooncologysequencingrnaseqgeneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationclusteringmultiplecomparisonqualitycontrolcpp

8.85 score 2 dependents 1.4k scripts 5.5k downloads

TitanCNA - Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.

Last updated 2 months ago

sequencingwholegenomednaseqexomeseqstatisticalmethodcopynumbervariationhiddenmarkovmodelgeneticsgenomicvariationimmunooncology10x-genomicscopy-number-variationgenome-sequencinghmmtumor-heterogeneity

8.45 score 94 stars 67 scripts 268 downloads

metaMS - MS-based metabolomics annotation pipeline

MS-based metabolomics data processing and compound annotation pipeline.

Last updated 2 months ago

immunooncologymassspectrometrymetabolomics

7.47 score 15 stars 14 scripts 417 downloads

shinyMethyl - Interactive visualization for Illumina methylation arrays

Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

Last updated 2 months ago

dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarray

7.44 score 5 stars 39 scripts 460 downloads

ASSIGN - Adaptive Signature Selection and InteGratioN (ASSIGN)

ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.

Last updated 2 months ago

softwaregeneexpressionpathwaysbayesian

7.37 score 2 stars 1 dependents 65 scripts 284 downloads

pRolocGUI - Interactive visualisation of spatial proteomics data

The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.

Last updated 2 months ago

proteomicsvisualizationgui

6.85 score 7 stars 3 scripts 239 downloads

GenomicFiles - Distributed computing by file or by range

This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

Last updated 2 months ago

geneticsinfrastructuredataimportsequencingcoverage

6.79 score 16 dependents 71 scripts 1.8k downloads

VariantFiltering - Filtering of coding and non-coding genetic variants

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

Last updated 2 months ago

geneticshomo_sapiensannotationsnpsequencinghighthroughputsequencing

6.13 score 4 stars 21 scripts 359 downloads

pepStat - Statistical analysis of peptide microarrays

Statistical analysis of peptide microarrays

Last updated 2 months ago

microarraypreprocessing

5.62 score 7 stars 4 scripts 223 downloads

ChIPQC - Quality metrics for ChIPseq data

Quality metrics for ChIPseq data.

Last updated 2 months ago

sequencingchipseqqualitycontrolreportwriting

5.44 score 137 scripts 592 downloads

riboSeqR - Analysis of sequencing data from ribosome profiling experiments

Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

Last updated 2 months ago

sequencinggeneticsvisualizationriboseq

5.37 score 14 scripts 338 downloads

flowDensity - Sequential Flow Cytometry Data Gating

This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.

Last updated 2 months ago

bioinformaticsflowcytometrycellbiologyclusteringcancerflowcytdatadatarepresentationstemcelldensitygating

5.17 score 3 dependents 83 scripts 436 downloads

HDTD - Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

Characterization of intra-individual variability using physiologically relevant measurements provides important insights into fundamental biological questions ranging from cell type identity to tumor development. For each individual, the data measurements can be written as a matrix with the different subsamples of the individual recorded in the columns and the different phenotypic units recorded in the rows. Datasets of this type are called high-dimensional transposable data. The HDTD package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.

Last updated 2 months ago

differentialexpressiongeneticsgeneexpressionmicroarraysequencingstatisticalmethodsoftwarebioconductor-packagehigh-dimensionalstatisticsopenblascppopenmp

4.78 score 1 stars 176 downloads

MeSHDbi - DBI to construct MeSH-related package from sqlite file

The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.

Last updated 2 months ago

annotationannotationdatainfrastructure

4.76 score 3 dependents 32 scripts 432 downloads

hiAnnotator - Functions for annotating GRanges objects

hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.

Last updated 2 months ago

softwareannotation

4.65 score 1 dependents 15 scripts 232 downloads

ABSSeq - ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level.

Last updated 2 months ago

differentialexpression

4.62 score 1 dependents 1 scripts 436 downloads

wavClusteR - Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).

Last updated 2 months ago

immunooncologysequencingtechnologyripseqrnaseqbayesian

4.60 score 3 scripts 341 downloads

meshr - Tools for conducting enrichment analysis of MeSH

A set of annotation maps describing the entire MeSH assembled using data from MeSH.

Last updated 2 months ago

annotationdatafunctionalannotationbioinformaticsstatisticsannotationmultiplecomparisonsmeshdb

4.56 score 1 dependents 9 scripts 290 downloads

flowClean - flowClean

A quality control tool for flow cytometry data based on compositional data analysis.

Last updated 2 months ago

flowcytometryqualitycontrolimmunooncology

4.53 score 17 scripts 369 downloads

MethylAid - Visual and interactive quality control of large Illumina DNA Methylation array data sets

A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Last updated 2 months ago

dnamethylationmethylationarraymicroarraytwochannelqualitycontrolbatcheffectvisualizationgui

4.51 score 16 scripts 366 downloads

Pviz - Peptide Annotation and Data Visualization using Gviz

Pviz adapts the Gviz package for protein sequences and data.

Last updated 2 months ago

visualizationproteomicsmicroarray

4.48 score 4 scripts 252 downloads

oposSOM - Comprehensive analysis of transcriptome data

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

Last updated 2 months ago

geneexpressiondifferentialexpressiongenesetenrichmentdatarepresentationvisualizationcpp

4.48 score 7 scripts 269 downloads

cosmiq - cosmiq - COmbining Single Masses Into Quantities

cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.

Last updated 2 months ago

immunooncologymassspectrometrymetabolomics

4.48 score 2 scripts 380 downloads

GSAR - Gene Set Analysis in R

Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.

Last updated 2 months ago

softwarestatisticalmethoddifferentialexpression

4.38 score 7 scripts 278 downloads

MultiMed - Testing multiple biological mediators simultaneously

Implements methods for testing multiple mediators

Last updated 2 months ago

multiplecomparisonstatisticalmethodsoftware

4.30 score 8 scripts 208 downloads

flowCyBar - Analyze flow cytometric data using gate information

A package to analyze flow cytometric data using gate information to follow population/community dynamics

Last updated 2 months ago

immunooncologycellbasedassaysclusteringflowcytometrysoftwarevisualization

4.15 score 1 scripts 192 downloads

GSReg - Gene Set Regulation (GS-Reg)

A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).

Last updated 2 months ago

generegulationpathwaysgeneexpressiongeneticvariabilitygenesetenrichmentalternativesplicing

3.98 score 16 scripts 206 downloads

ssviz - A small RNA-seq visualizer and analysis toolkit

Small RNA sequencing viewer

Last updated 2 months ago

immunooncologysequencingrnaseqvisualizationmultiplecomparisongenetics

3.60 score 2 scripts 244 downloads

RGSEA - Random Gene Set Enrichment Analysis

Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements.

Last updated 2 months ago

genesetenrichmentstatisticalmethodclassification

3.30 score 1 scripts 239 downloads

blima - Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

Last updated 2 months ago

microarraypreprocessingnormalizationdifferentialexpressiongeneregulationgeneexpressioncpp

3.30 score 1 scripts 238 downloads

fastLiquidAssociation - functions for genome-wide application of Liquid Association

This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.

Last updated 2 months ago

softwaregeneexpressiongeneticspathwayscellbiology

3.30 score 3 scripts 242 downloads

npGSEA - Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

Last updated 2 months ago

genesetenrichmentmicroarraystatisticalmethodpathways

3.30 score 4 scripts 242 downloads

FRGEpistasis - Epistasis Analysis for Quantitative Traits by Functional Regression Model

A Tool for Epistasis Analysis Based on Functional Regression Model

Last updated 2 months ago

geneticsnetworkinferencegeneticvariabilitysoftware

3.30 score 6 scripts 183 downloads

CoverageView - Coverage visualization package for R

This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome

Last updated 2 months ago

immunooncologyvisualizationrnaseqchipseqsequencingtechnologysoftware

2.78 score 5 scripts 331 downloads

Biobase - Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

Last updated 2 months ago

infrastructurebioconductor-packagecore-package

16.50 score 9 stars 1.8k dependents 7.0k scripts 98k downloads

goseq - Gene Ontology analyser for RNA-seq and other length biased data

Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

Last updated 2 months ago

immunooncologysequencinggogeneexpressiontranscriptionrnaseqdifferentialexpressionannotationgenesetenrichmentkeggpathwayssoftware

9.79 score 9 dependents 636 scripts 2.3k downloads

gage - Generally Applicable Gene-set Enrichment for Pathway Analysis

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

Last updated 2 months ago

pathwaysgodifferentialexpressionmicroarrayonechanneltwochannelrnaseqgeneticsmultiplecomparisongenesetenrichmentgeneexpressionsystemsbiologysequencing

8.58 score 5 stars 1 dependents 584 scripts 1.4k downloads

ConsensusClusterPlus - ConsensusClusterPlus

algorithm for determining cluster count and membership by stability evidence in unsupervised analysis

Last updated 2 months ago

softwareclustering

8.35 score 22 dependents 402 scripts 4.2k downloads

CoGAPS - Coordinated Gene Activity in Pattern Sets

Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

Last updated 2 months ago

geneexpressiontranscriptiongenesetenrichmentdifferentialexpressionbayesianclusteringtimecoursernaseqmicroarraymultiplecomparisondimensionreductionimmunooncologycpp

6.80 score 104 scripts 576 downloads

PICS - Probabilistic inference of ChIP-seq

Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

Last updated 2 months ago

clusteringvisualizationsequencingchipseqgsl

6.26 score 1 dependents 7 scripts 310 downloads

BioNet - Routines for the functional analysis of biological networks

This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.

Last updated 2 months ago

microarraydataimportgraphandnetworknetworknetworkenrichmentgeneexpressiondifferentialexpression

6.14 score 2 dependents 114 scripts 628 downloads

fabia - FABIA: Factor Analysis for Bicluster Acquisition

Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.

Last updated 2 months ago

statisticalmethodmicroarraydifferentialexpressionmultiplecomparisonclusteringvisualization

5.84 score 6 dependents 32 scripts 358 downloads

netresponse - Functional Network Analysis

Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.

Last updated 2 months ago

cellbiologyclusteringgeneexpressiongeneticsnetworkgraphandnetworkdifferentialexpressionmicroarraynetworkinferencetranscription

5.64 score 3 stars 21 scripts 258 downloads

flowMeans - Non-parametric Flow Cytometry Data Gating

Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.

Last updated 2 months ago

immunooncologyflowcytometrycellbiologyclustering

5.62 score 2 dependents 35 scripts 408 downloads

PROMISE - PRojection Onto the Most Interesting Statistical Evidence

A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019

Last updated 2 months ago

microarrayonechannelmultiplecomparisongeneexpression

5.44 score 1 dependents 46 scripts 284 downloads

NuPoP - An R package for nucleosome positioning prediction

NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.

Last updated 2 months ago

geneticsvisualizationclassificationnucleosomepositioninghiddenmarkovmodelfortran

5.04 score 11 scripts 233 downloads

rGADEM - de novo motif discovery

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.

Last updated 2 months ago

microarraychipchipsequencingchipseqmotifdiscoveryopenmp

4.95 score 56 scripts 686 downloads

RDRToolbox - A package for nonlinear dimension reduction with Isomap and LLE.

A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset.

Last updated 2 months ago

dimensionreductionfeatureextractionvisualizationclusteringmicroarray

4.87 score 53 scripts 392 downloads

BeadDataPackR - Compression of Illumina BeadArray data

Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

Last updated 2 months ago

microarray

4.79 score 5 dependents 2 scripts 1.0k downloads

flowTrans - Parameter Optimization for Flow Cytometry Data Transformation

Profile maximum likelihood estimation of parameters for flow cytometry data transformations.

Last updated 2 months ago

immunooncologyflowcytometry

4.40 score 21 scripts 272 downloads

tigre - Transcription factor Inference through Gaussian process Reconstruction of Expression

The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.

Last updated 2 months ago

microarraytimecoursegeneexpressiontranscriptiongeneregulationnetworkinferencebayesian

4.38 score 6 scripts 311 downloads

iSeq - Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models

Bayesian hidden Ising models are implemented to identify IP-enriched genomic regions from ChIP-seq data. They can be used to analyze ChIP-seq data with and without controls and replicates.

Last updated 2 months ago

chipseqsequencing

4.30 score 2 scripts 191 downloads

MassArray - Analytical Tools for MassArray Data

This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.

Last updated 2 months ago

immunooncologydnamethylationsnpmassspectrometrygeneticsdataimportvisualization

4.30 score 1 scripts 190 downloads

genoCN - genotyping and copy number study tools

Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations

Last updated 2 months ago

microarraygenetics

4.15 score 5 scripts 206 downloads

iChip - Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models

Hidden Ising models are implemented to identify enriched genomic regions in ChIP-chip data. They can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.

Last updated 2 months ago

chipchiponechannelagilentchipmicroarray

4.15 score 3 scripts 254 downloads

CRImage - CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

Last updated 2 months ago

cellbiologyclassification

4.00 score 6 scripts 292 downloads

les - Identifying Differential Effects in Tiling Microarray Data

The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

Last updated 2 months ago

microarraydifferentialexpressionchipchipdnamethylationtranscription

3.78 score 1 dependents 3 scripts 272 downloads

NTW - Predict gene network using an Ordinary Differential Equation (ODE) based method

This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.

Last updated 2 months ago

preprocessing

3.78 score 1 scripts 219 downloads

hyperdraw - Visualizing Hypergaphs

Functions for visualizing hypergraphs.

Last updated 2 months ago

visualizationgraphandnetwork

3.78 score 1 dependents 3 scripts 375 downloads

affyILM - Linear Model of background subtraction and the Langmuir isotherm

affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.

Last updated 2 months ago

microarrayonechannelpreprocessing

3.60 score 1 scripts 412 downloads

ADaCGH2 - Analysis of big data from aCGH experiments using parallel computing and ff objects

Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Last updated 2 months ago

microarraycopynumbervariants

3.48 score 3 scripts 382 downloads

R453Plus1Toolbox - A package for importing and analyzing data from Roche's Genome Sequencer System

The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

Last updated 2 months ago

sequencinginfrastructuredataimportdatarepresentationvisualizationqualitycontrolreportwriting

3.48 score 10 scripts 261 downloads

genomes - Genome sequencing project metadata

Download genome and assembly reports from NCBI

Last updated 2 months ago

annotationgenetics

3.48 score 15 scripts 253 downloads

OTUbase - Provides structure and functions for the analysis of OTU data

Provides a platform for Operational Taxonomic Unit based analysis

Last updated 2 months ago

sequencingdataimport

3.30 score 257 downloads

attract - Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.

Last updated 2 months ago

immunooncologykeggreactomegeneexpressionpathwaysgenesetenrichmentmicroarrayrnaseq

3.30 score 4 scripts 382 downloads

GSRI - Gene Set Regulation Index

The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).

Last updated 2 months ago

microarraytranscriptiondifferentialexpressiongenesetenrichmentgeneregulation

3.30 score 2 scripts 283 downloads

GEOsubmission - Prepares microarray data for submission to GEO

Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).

Last updated 2 months ago

microarray

3.30 score 2 scripts 246 downloads

MBCB - MBCB (Model-based Background Correction for Beadarray)

This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.

Last updated 2 months ago

microarraypreprocessing

3.08 score 12 scripts 236 downloads

Mulcom - Calculates Mulcom test

Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test.

Last updated 2 months ago

statisticalmethodmultiplecomparisonmicroarraydifferentialexpressiongeneexpressioncpp

3.00 score 280 downloads

GeneGA - Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm

R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.

Last updated 2 months ago

geneexpression

2.30 score 6 scripts 164 downloads

GOSemSim - GO-terms Semantic Similarity Measures

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.

Last updated 2 months ago

annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similaritycpp

14.24 score 60 stars 70 dependents 712 scripts 30k downloads

rtracklayer - R interface to genome annotation files and the UCSC genome browser

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

Last updated 2 months ago

annotationvisualizationdataimportzlibopensslcurl

12.62 score 483 dependents 6.8k scripts 43k downloads

ShortRead - FASTQ input and manipulation

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

Last updated 2 months ago

dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp

12.28 score 8 stars 51 dependents 1.8k scripts 11k downloads

ChemmineR - Cheminformatics Toolkit for R

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

Last updated 2 months ago

cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp

10.40 score 13 stars 13 dependents 238 scripts 1.5k downloads

KEGGgraph - KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

Last updated 2 months ago

pathwaysgraphandnetworkvisualizationkegg

9.08 score 25 dependents 108 scripts 7.5k downloads

flowClust - Clustering for Flow Cytometry

Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.

Last updated 2 months ago

immunooncologyclusteringvisualizationflowcytometry

7.44 score 6 dependents 82 scripts 1.3k downloads

qpgraph - Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

Last updated 2 months ago

microarraygeneexpressiontranscriptionpathwaysnetworkinferencegraphandnetworkgeneregulationgeneticsgeneticvariabilitysnpsoftwareopenblas

7.08 score 3 dependents 20 scripts 421 downloads

minet - Mutual Information NETworks

This package implements various algorithms for inferring mutual information networks from data.

Last updated 2 months ago

microarraygraphandnetworknetworknetworkinferencecpp

6.15 score 16 dependents 114 scripts 1.3k downloads

ArrayExpress - Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet.

Last updated 2 months ago

microarraydataimportonechanneltwochannel

5.88 score 1 dependents 125 scripts 864 downloads

goProfiles - goProfiles: an R package for the statistical analysis of functional profiles

The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.

Last updated 2 months ago

annotationgogeneexpressiongenesetenrichmentgraphandnetworkmicroarraymultiplecomparisonpathwayssoftware

5.48 score 1 dependents 6 scripts 358 downloads

HELP - Tools for HELP data analysis

The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.

Last updated 2 months ago

cpgislanddnamethylationmicroarraytwochanneldataimportqualitycontrolpreprocessingvisualization

5.15 score 71 scripts 254 downloads

CMA - Synthesis of microarray-based classification

This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.

Last updated 2 months ago

classificationdecisiontree

5.09 score 61 scripts 342 downloads

parody - Parametric And Resistant Outlier DYtection

Provide routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

Last updated 2 months ago

multiplecomparison

4.73 score 1 dependents 12 scripts 425 downloads

HilbertVis - Hilbert curve visualization

Functions to visualize long vectors of integer data by means of Hilbert curves

Last updated 2 months ago

visualization

4.40 score 1 dependents 14 scripts 367 downloads

CGHregions - Dimension Reduction for Array CGH Data with Minimal Information Loss.

Dimension Reduction for Array CGH Data with Minimal Information Loss

Last updated 2 months ago

microarraycopynumbervariationvisualization

4.32 score 26 scripts 284 downloads

flagme - Analysis of Metabolomics GC/MS Data

Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.

Last updated 2 months ago

differentialexpressionmassspectrometry

4.30 score 2 scripts 258 downloads

MEDME - Modelling Experimental Data from MeDIP Enrichment

MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments

Last updated 2 months ago

microarraycpgislanddnamethylation

4.30 score 2 scripts 295 downloads

miRNApath - miRNApath: Pathway Enrichment for miRNA Expression Data

This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.

Last updated 2 months ago

annotationpathwaysdifferentialexpressionnetworkenrichmentmirna

4.30 score 3 scripts 219 downloads

SIM - Integrated Analysis on two human genomic datasets

Finds associations between two human genomic datasets.

Last updated 2 months ago

microarrayvisualization

4.30 score 3 scripts 299 downloads

BicARE - Biclustering Analysis and Results Exploration

Biclustering Analysis and Results Exploration.

Last updated 2 months ago

microarraytranscriptionclustering

4.08 score 2 dependents 2 scripts 430 downloads

ITALICS - ITALICS

A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set

Last updated 2 months ago

microarraycopynumbervariation

4.08 score 388 downloads

multiscan - R package for combining multiple scans

Estimates gene expressions from several laser scans of the same microarray

Last updated 2 months ago

microarraypreprocessing

4.08 score 2 scripts 266 downloads

affyContam - structured corruption of affymetrix cel file data

structured corruption of cel file data to demonstrate QA effectiveness

Last updated 2 months ago

infrastructure

3.78 score 1 dependents 1 scripts 460 downloads

KCsmart - Multi sample aCGH analysis package using kernel convolution

Multi sample aCGH analysis package using kernel convolution

Last updated 2 months ago

copynumbervariationvisualizationacghmicroarray

3.60 score 1 scripts 306 downloads

arrayMvout - multivariate outlier detection for expression array QA

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate

Last updated 2 months ago

infrastructuremicroarrayqualitycontrol

3.34 score 11 scripts 386 downloads

spkTools - Methods for Spike-in Arrays

The package contains functions that can be used to compare expression measures on different array platforms.

Last updated 2 months ago

softwaretechnologymicroarray

3.30 score 1 scripts 260 downloads

biomaRt - Interface to BioMart databases (i.e. Ensembl)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

Last updated 2 months ago

annotationbioconductorbiomartensembl

15.88 score 36 stars 228 dependents 13k scripts 38k downloads

DelayedArray - A unified framework for working transparently with on-disk and in-memory array-like datasets

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.

Last updated 19 days ago

infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-package

15.64 score 26 stars 1.2k dependents 554 scripts 92k downloads

GenomicAlignments - Representation and manipulation of short genomic alignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Last updated 2 months ago

infrastructuredataimportgeneticssequencingrnaseqsnpcoveragealignmentimmunooncologybioconductor-packagecore-package

15.49 score 9 stars 530 dependents 3.0k scripts 46k downloads

Rsamtools - Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Last updated 25 days ago

dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp

15.48 score 27 stars 572 dependents 3.2k scripts 48k downloads

GenomicFeatures - Query the gene models of a given organism/assembly

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

Last updated 2 months ago

geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package

15.40 score 26 stars 341 dependents 5.3k scripts 34k downloads

DOSE - Disease Ontology Semantic and Enrichment analysis

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

Last updated 2 months ago

annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity

15.09 score 118 stars 64 dependents 1.9k scripts 29k downloads

AnnotationDbi - Manipulation of SQLite-based annotations in Bioconductor

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Last updated 2 months ago

annotationmicroarraysequencinggenomeannotationbioconductor-packagecore-package

15.02 score 9 stars 775 dependents 3.2k scripts 70k downloads

GEOquery - Get data from NCBI Gene Expression Omnibus (GEO)

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

Last updated 2 months ago

microarraydataimportonechanneltwochannelsagebioconductorbioinformaticsdata-sciencegenomicsncbi-geo

14.55 score 88 stars 54 dependents 4.3k scripts 15k downloads

KEGGREST - Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)

A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see <https://www.kegg.jp/kegg/rest/>). Note that KEGGREST is based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.

Last updated 2 months ago

annotationpathwaysthirdpartyclientkeggbioconductor-packagecore-package

14.40 score 8 stars 782 dependents 674 scripts 67k downloads

BSgenome - Software infrastructure for efficient representation of full genomes and their SNPs

Infrastructure shared by all the Biostrings-based genome data packages.

Last updated 2 months ago

geneticsinfrastructuredatarepresentationsequencematchingannotationsnpbioconductor-packagecore-package

14.13 score 9 stars 272 dependents 1.1k scripts 27k downloads

qvalue - Q-value estimation for false discovery rate control

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Last updated 2 months ago

multiplecomparisons

14.11 score 113 stars 140 dependents 3.2k scripts 28k downloads

BiocGenerics - S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

Last updated 1 months ago

infrastructurebioconductor-packagecore-package

14.06 score 12 stars 2.2k dependents 606 scripts 113k downloads

ensembldb - Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Last updated 2 months ago

geneticsannotationdatasequencingcoverageannotationbioconductorbioconductor-packagesensembl

14.05 score 33 stars 110 dependents 876 scripts 17k downloads

phyloseq - Handling and analysis of high-throughput microbiome census data

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Last updated 2 months ago

immunooncologysequencingmicrobiomemetagenomicsclusteringclassificationmultiplecomparisongeneticvariability

13.87 score 586 stars 36 dependents 8.3k scripts 9.5k downloads

limma - Linear Models for Microarray and Omics Data

Data analysis, linear models and differential expression for omics data.

Last updated 1 months ago

exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics

13.80 score 583 dependents 15k scripts 63k downloads

edgeR - Empirical Analysis of Digital Gene Expression Data in R

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.

Last updated 22 days ago

geneexpressiontranscriptionalternativesplicingcoveragedifferentialexpressiondifferentialsplicingdifferentialmethylationgenesetenrichmentpathwaysgeneticsdnamethylationbayesianclusteringchipseqregressiontimecoursesequencingrnaseqbatcheffectsagenormalizationqualitycontrolmultiplecomparisonbiomedicalinformaticscellbiologyfunctionalgenomicsepigeneticsimmunooncologysystemsbiologytranscriptomicssinglecellopenblas

13.49 score 253 dependents 16k scripts 44k downloads

SingleCellExperiment - S4 Classes for Single Cell Data

Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

Last updated 1 months ago

immunooncologydatarepresentationdataimportinfrastructuresinglecell

13.41 score 270 dependents 14k scripts 30k downloads

minfi - Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

Last updated 1 months ago

immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol

13.12 score 60 stars 34 dependents 1.1k scripts 4.4k downloads

Gviz - Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Last updated 2 months ago

visualizationmicroarraysequencing

13.06 score 75 stars 50 dependents 1.4k scripts 5.7k downloads

pcaMethods - A collection of PCA methods

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.

Last updated 2 months ago

bayesiancpp

13.04 score 46 stars 72 dependents 506 scripts 8.1k downloads

EBImage - Image processing and analysis toolbox for R

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

Last updated 2 months ago

visualizationbioinformaticsimage-analysisimage-processingcpp

12.90 score 71 stars 33 dependents 1.5k scripts 4.3k downloads

MSnbase - Base Functions and Classes for Mass Spectrometry and Proteomics

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

Last updated 1 months ago

immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp

12.81 score 127 stars 35 dependents 712 scripts 5.6k downloads

SNPRelate - Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls in whole-genome and whole-exome variant data.

Last updated 2 months ago

infrastructuregeneticsstatisticalmethodprincipalcomponentbioinformaticsgds-formatpcasimdsnpopenblascpp

12.76 score 101 stars 18 dependents 1.5k scripts 2.9k downloads

mzR - parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

Last updated 1 months ago

immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometry

12.62 score 42 stars 43 dependents 188 scripts 5.6k downloads

SparseArray - High-performance sparse data representation and manipulation in R

The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.

Last updated 1 months ago

infrastructuredatarepresentationbioconductor-packagecore-packageopenmp

12.45 score 8 stars 1.2k dependents 45 scripts 77k downloads

ggbio - Visualization tools for genomic data

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Last updated 2 months ago

infrastructurevisualization

12.27 score 111 stars 18 dependents 714 scripts 4.4k downloads

ReactomePA - Reactome Pathway Analysis

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. This package is not affiliated with the Reactome team.

Last updated 2 months ago

pathwaysvisualizationannotationmultiplecomparisongenesetenrichmentreactomeenrichment-analysisreactome-pathway-analysisreactomepa

12.22 score 39 stars 7 dependents 1.1k scripts 4.1k downloads

HDF5Array - HDF5 datasets as array-like objects in R

The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.

Last updated 22 days ago

infrastructuredatarepresentationdataimportsequencingrnaseqcoverageannotationgenomeannotationsinglecellimmunooncologybioconductor-packagecore-packageopensslcurlzlib

12.10 score 11 stars 131 dependents 804 scripts 27k downloads

SeqArray - Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

Last updated 2 months ago

infrastructuredatarepresentationsequencinggeneticsbioinformaticsgds-formatsnpsnvweswgscpp

12.04 score 44 stars 9 dependents 1.1k scripts 1.6k downloads

TFBSTools - Software Package for Transcription Factor Binding Site (TFBS) Analysis

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Last updated 2 months ago

motifannotationgeneregulationmotifdiscoverytranscriptionalignment

12.00 score 25 stars 18 dependents 1000 scripts 7.1k downloads

preprocessCore - A collection of pre-processing functions

A library of core preprocessing routines.

Last updated 2 months ago

infrastructureopenblas

12.00 score 17 stars 212 dependents 1.8k scripts 22k downloads

bumphunter - Bump Hunter

Tools for finding bumps in genomic data

Last updated 2 months ago

dnamethylationepigeneticsinfrastructuremultiplecomparisonimmunooncology

11.84 score 16 stars 50 dependents 222 scripts 4.7k downloads

annotate - Annotation for microarrays

Using R enviroments for annotation.

Last updated 2 months ago

annotationpathwaysgo

11.74 score 254 dependents 792 scripts 32k downloads

variancePartition - Quantify and interpret drivers of variation in multilevel gene expression experiments

Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.

Last updated 1 months ago

rnaseqgeneexpressiongenesetenrichmentdifferentialexpressionbatcheffectqualitycontrolregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationpreprocessingmicroarrayimmunooncologysoftware

11.63 score 5 stars 3 dependents 1.1k scripts 1.7k downloads

graph - graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Last updated 2 months ago

graphandnetwork

11.57 score 341 dependents 796 scripts 31k downloads

systemPipeR - systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.

Last updated 2 months ago

geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement

11.55 score 52 stars 3 dependents 336 scripts 2.0k downloads

msa - Multiple Sequence Alignment

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

Last updated 2 months ago

multiplesequencealignmentalignmentmultiplecomparisonsequencingcpp

11.49 score 17 stars 6 dependents 748 scripts 3.3k downloads

methylKit - DNA methylation analysis from high-throughput bisulfite sequencing results

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.

Last updated 25 days ago

dnamethylationsequencingmethylseqgenome-biologymethylationstatistical-analysisvisualizationcurlbzip2xz-utilszlibcpp

11.48 score 213 stars 3 dependents 572 scripts 1.2k downloads

VariantAnnotation - Annotation of Genetic Variants

Annotate variants, compute amino acid coding changes, predict coding outcomes.

Last updated 2 months ago

dataimportsequencingsnpannotationgeneticsvariantannotation

11.47 score 157 dependents 1.9k scripts 16k downloads

mia - Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Last updated 1 months ago

microbiomesoftwaredataimportanalysisbioconductor

11.42 score 51 stars 4 dependents 356 scripts 2.6k downloads

S4Arrays - Foundation of array-like containers in Bioconductor

The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).

Last updated 2 months ago

infrastructuredatarepresentationbioconductor-packagecore-package

11.34 score 5 stars 1.2k dependents 7 scripts 75k downloads

Rhtslib - HTSlib high-throughput sequencing library as an R package

This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").

Last updated 25 days ago

dataimportsequencingbioconductor-packagecore-packagecurlbzip2xz-utilszlib

11.34 score 11 stars 594 dependents 3 scripts 46k downloads

genefilter - genefilter: methods for filtering genes from high-throughput experiments

Some basic functions for filtering genes.

Last updated 2 months ago

microarrayfortrancpp

11.32 score 152 dependents 2.4k scripts 21k downloads

BiocStyle - Standard styles for vignettes and other Bioconductor documents

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

Last updated 2 months ago

softwarebioconductor-packagecore-package

11.31 score 12 stars 46 dependents 1.2k scripts 10k downloads

pathview - a tool set for pathway based data integration and visualization

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Last updated 2 months ago

pathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing

11.28 score 38 stars 12 dependents 1.5k scripts 6.3k downloads

Rgraphviz - Provides plotting capabilities for R graph objects

Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

Last updated 2 months ago

graphandnetworkvisualizationzlib

11.25 score 113 dependents 1.3k scripts 14k downloads

gdsfmt - R Interface to CoreArray Genomic Data Structure (GDS) Files

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

Last updated 2 months ago

infrastructuredataimportbioinformaticsgds-formatgenomicscpp

11.25 score 18 stars 30 dependents 922 scripts 3.4k downloads

genomation - Summary, annotation and visualization of genomic data

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Last updated 2 months ago

annotationsequencingvisualizationcpgislandcpp

11.07 score 74 stars 5 dependents 730 scripts 1.0k downloads

CATALYST - Cytometry dATa anALYSis Tools

CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.

Last updated 23 days ago

clusteringdataimportdifferentialexpressionexperimentaldesignflowcytometryimmunooncologymassspectrometrynormalizationpreprocessingsinglecellsoftwarestatisticalmethodvisualization

11.05 score 66 stars 2 dependents 362 scripts 1.1k downloads

affy - Methods for Affymetrix Oligonucleotide Arrays

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Last updated 2 months ago

microarrayonechannelpreprocessing

11.03 score 103 dependents 2.4k scripts 12k downloads

zellkonverter - Conversion Between scRNA-seq Objects

Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.

Last updated 30 days ago

singlecelldataimportdatarepresentationbioconductorconversionscrna-seq

11.01 score 151 stars 4 dependents 540 scripts 2.3k downloads

destiny - Creates diffusion maps

Create and plot diffusion maps.

Last updated 1 months ago

cellbiologycellbasedassaysclusteringsoftwarevisualizationdiffusion-mapsdimensionality-reductioncpp

11.00 score 79 stars 784 scripts 1.1k downloads

DirichletMultinomial - Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

Last updated 2 months ago

immunooncologymicrobiomesequencingclusteringclassificationmetagenomicsgsl

10.97 score 11 stars 25 dependents 125 scripts 9.5k downloads

universalmotif - Import, Modify, and Export Motifs with R

Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.

Last updated 1 months ago

motifannotationmotifdiscoverydataimportgeneregulationmotif-analysismotif-enrichment-analysissequence-logocpp

10.96 score 25 stars 11 dependents 286 scripts 1.3k downloads

ALDEx2 - Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.

Last updated 2 months ago

differentialexpressionrnaseqtranscriptomicsgeneexpressiondnaseqchipseqbayesiansequencingsoftwaremicrobiomemetagenomicsimmunooncologyscale simulationposterior p-value

10.79 score 27 stars 4 dependents 426 scripts 2.0k downloads

flowCore - flowCore: Basic structures for flow cytometry data

Provides S4 data structures and basic functions to deal with flow cytometry data.

Last updated 2 months ago

immunooncologyinfrastructureflowcytometrycellbasedassayscpp

10.64 score 59 dependents 1.7k scripts 4.7k downloads

UCell - Rank-based signature enrichment analysis for single-cell data

UCell is a package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.

Last updated 2 months ago

singlecellgenesetenrichmenttranscriptomicsgeneexpressioncellbasedassays

10.61 score 140 stars 2 dependents 422 scripts 2.4k downloads

seqLogo - Sequence logos for DNA sequence alignments

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

Last updated 2 months ago

sequencematching

10.55 score 4 stars 29 dependents 302 scripts 5.6k downloads

ballgown - Flexible, isoform-level differential expression analysis

Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

Last updated 2 months ago

immunooncologyrnaseqstatisticalmethodpreprocessingdifferentialexpression

10.49 score 142 stars 1 dependents 334 scripts 1.8k downloads

GWASTools - Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Last updated 2 months ago

snpgeneticvariabilityqualitycontrolmicroarray

10.48 score 17 stars 5 dependents 388 scripts 1.1k downloads

CAMERA - Collection of annotation related methods for mass spectrometry data

Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments

Last updated 2 months ago

immunooncologymassspectrometrymetabolomics

10.37 score 11 stars 6 dependents 165 scripts 820 downloads

pRoloc - A unifying bioinformatics framework for spatial proteomics

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

Last updated 29 days ago

immunooncologyproteomicsmassspectrometryclassificationclusteringqualitycontrolbioconductorproteomics-dataspatial-proteomicsvisualisation

10.36 score 15 stars 2 dependents 100 scripts 471 downloads

illuminaio - Parsing Illumina Microarray Output Files

Tools for parsing Illumina's microarray output files, including IDAT.

Last updated 2 months ago

infrastructuredataimportmicroarrayproprietaryplatformsbioconductor

10.36 score 6 stars 44 dependents 46 scripts 4.5k downloads

oligo - Preprocessing tools for oligonucleotide arrays

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Last updated 2 months ago

microarrayonechanneltwochannelpreprocessingsnpdifferentialexpressionexonarraygeneexpressiondataimportzlib

10.32 score 3 stars 11 dependents 532 scripts 2.6k downloads

EpiDISH - Epigenetic Dissection of Intra-Sample-Heterogeneity

EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of blood-tissue of any age, from birth to old-age, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.

Last updated 1 months ago

dnamethylationmethylationarrayepigeneticsdifferentialmethylationimmunooncology

10.26 score 45 stars 4 dependents 169 scripts 1.1k downloads

EDASeq - Exploratory Data Analysis and Normalization for RNA-Seq

Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

Last updated 2 months ago

immunooncologysequencingrnaseqpreprocessingqualitycontroldifferentialexpression

10.26 score 5 stars 9 dependents 602 scripts 2.8k downloads

GSEABase - Gene set enrichment data structures and methods

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

Last updated 2 months ago

geneexpressiongenesetenrichmentgraphandnetworkgokegg

10.26 score 78 dependents 1.4k scripts 13k downloads

BiocIO - Standard Input and Output for Bioconductor Packages

The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.

Last updated 1 months ago

annotationdataimportbioconductor-packagecore-package

10.23 score 1 stars 494 dependents 19 scripts 33k downloads

rGREAT - GREAT Analysis - Functional Enrichment on Genomic Regions

GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.

Last updated 2 months ago

genesetenrichmentgopathwayssoftwaresequencingwholegenomegenomeannotationcoveragecpp

10.22 score 85 stars 1 dependents 322 scripts 974 downloads

GENESIS - GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.

Last updated 2 months ago

snpgeneticvariabilitygeneticsstatisticalmethoddimensionreductionprincipalcomponentgenomewideassociationqualitycontrolbiocviews

10.19 score 34 stars 1 dependents 340 scripts 614 downloads

BiocCheck - Bioconductor-specific package checks

BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.

Last updated 1 months ago

infrastructurebioconductor-packagecore-services

10.15 score 8 stars 6 dependents 115 scripts 3.7k downloads

graphite - GRAPH Interaction from pathway Topological Environment

Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.

Last updated 2 months ago

pathwaysthirdpartyclientgraphandnetworknetworkreactomekeggmetabolomicsbioinformaticsmirrorpathway-analysis

10.09 score 6 stars 21 dependents 120 scripts 4.3k downloads

methylumi - Handle Illumina methylation data

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Last updated 2 months ago

dnamethylationtwochannelpreprocessingqualitycontrolcpgisland

10.09 score 8 stars 16 dependents 85 scripts 2.7k downloads

sva - Surrogate Variable Analysis

The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).

Last updated 2 months ago

immunooncologymicroarraystatisticalmethodpreprocessingmultiplecomparisonsequencingrnaseqbatcheffectnormalization

10.08 score 52 dependents 3.4k scripts 11k downloads

QDNAseq - Quantitative DNA Sequencing for Chromosomal Aberrations

Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Last updated 2 months ago

copynumbervariationdnaseqgeneticsgenomeannotationpreprocessingqualitycontrolsequencing

10.08 score 49 stars 4 dependents 170 scripts 660 downloads

splatter - Simple Simulation of Single-cell RNA Sequencing Data

Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

Last updated 30 days ago

singlecellrnaseqtranscriptomicsgeneexpressionsequencingsoftwareimmunooncologybioconductorbioinformaticsscrna-seqsimulation

9.91 score 219 stars 1 dependents 424 scripts 801 downloads

biocViews - Categorized views of R package repositories

Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages.

Last updated 2 months ago

infrastructurebioconductor-packagecore-package

9.71 score 4 stars 14 dependents 30 scripts 7.1k downloads

RBGL - An interface to the BOOST graph library

A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

Last updated 2 months ago

graphandnetworknetworkcpp

9.59 score 134 dependents 316 scripts 15k downloads

DNAcopy - DNA Copy Number Data Analysis

Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

Last updated 2 months ago

microarraycopynumbervariationfortran

9.53 score 64 dependents 234 scripts 7.5k downloads

txdbmaker - Tools for making TxDb objects from genomic annotations

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

Last updated 30 days ago

infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package

9.49 score 2 stars 87 dependents 82 scripts 4.8k downloads

AnnotationForge - Tools for building SQLite-based annotation data packages

Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

Last updated 2 months ago

annotationinfrastructurebioconductor-packagecore-package

9.47 score 4 stars 20 dependents 150 scripts 3.1k downloads

snpStats - SnpMatrix and XSnpMatrix classes and methods

Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

Last updated 2 months ago

microarraysnpgeneticvariabilityzlib

9.43 score 17 dependents 702 scripts 3.2k downloads

multtest - Resampling-based multiple hypothesis testing

Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

Last updated 2 months ago

microarraydifferentialexpressionmultiplecomparison

9.39 score 145 dependents 960 scripts 19k downloads

EnrichmentBrowser - Seamless navigation through combined results of set-based and network-based enrichment analysis

The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

Last updated 2 months ago

immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwriting

9.37 score 20 stars 3 dependents 164 scripts 949 downloads

GenomicInteractions - Utilities for handling genomic interaction data

Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.

Last updated 2 months ago

softwareinfrastructuredataimportdatarepresentationhic

9.37 score 7 stars 6 dependents 155 scripts 834 downloads

flowWorkspace - Infrastructure for representing and interacting with gated and ungated cytometry data sets.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Last updated 2 months ago

immunooncologyflowcytometrydataimportpreprocessingdatarepresentationzlibopenblascpp

9.36 score 10 dependents 580 scripts 2.2k downloads

CNEr - CNE Detection and Visualization

Large-scale identification and advanced visualization of sets of conserved noncoding elements.

Last updated 2 months ago

generegulationvisualizationdataimport

9.29 score 3 stars 19 dependents 35 scripts 6.0k downloads

impute - impute: Imputation for microarray data

Imputation for microarray data (currently KNN only)

Last updated 2 months ago

microarrayfortran

9.00 score 131 dependents 860 scripts 15k downloads

regioneR - Association analysis of genomic regions based on permutation tests

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

Last updated 2 months ago

geneticschipseqdnaseqmethylseqcopynumbervariation

8.97 score 21 dependents 2.6k scripts 2.9k downloads

bamsignals - Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Last updated 2 months ago

dataimportsequencingcoveragealignmentcurlbzip2xz-utilszlibcpp

8.95 score 13 stars 12 dependents 31 scripts 1.5k downloads

RaggedExperiment - Representation of Sparse Experiments and Assays Across Samples

This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.

Last updated 29 days ago

infrastructuredatarepresentationcopynumbercore-packagedata-structuremutations

8.94 score 4 stars 13 dependents 74 scripts 1.4k downloads

topGO - Enrichment Analysis for Gene Ontology

topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Last updated 2 months ago

microarrayvisualization

8.94 score 20 dependents 1.8k scripts 4.0k downloads

marray - Exploratory analysis for two-color spotted microarray data

Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.

Last updated 2 months ago

microarraytwochannelpreprocessing

8.92 score 38 dependents 222 scripts 2.7k downloads

ChIPpeakAnno - Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Last updated 2 months ago

annotationchipseqchipchip

8.85 score 6 dependents 544 scripts 1.8k downloads

affxparser - Affymetrix File Parsing SDK

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

Last updated 2 months ago

infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductorcpp

8.83 score 7 stars 15 dependents 65 scripts 2.4k downloads

iCOBRA - Comparison and Visualization of Ranking and Assignment Methods

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. Various types of performance plots can be generated programmatically. The package also contains a shiny application for interactive exploration of results.

Last updated 2 months ago

classificationvisualization

8.78 score 14 stars 1 dependents 192 scripts 596 downloads

SeqVarTools - Tools for variant data

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

Last updated 2 months ago

snpgeneticvariabilitysequencinggenetics

8.76 score 3 stars 2 dependents 384 scripts 763 downloads

rols - An R interface to the Ontology Lookup Service

The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.

Last updated 2 months ago

immunooncologysoftwareannotationmassspectrometrygo

8.59 score 11 stars 5 dependents 87 scripts 722 downloads

Voyager - From geospatial to spatial omics

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.

Last updated 19 days ago

geneexpressionspatialtranscriptomicsvisualizationbioconductoredaesdaexploratory-data-analysisomicsspatial-statisticsspatial-transcriptomics

8.53 score 79 stars 133 scripts 302 downloads

survcomp - Performance Assessment and Comparison for Survival Analysis

Assessment and Comparison for Performance of Risk Prediction (Survival) Models.

Last updated 2 months ago

geneexpressiondifferentialexpressionvisualizationcpp

8.49 score 12 dependents 452 scripts 1.9k downloads

alabaster.base - Save Bioconductor Objects to File

Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 1 months ago

datarepresentationdataimportzlibcpp

8.49 score 3 stars 14 dependents 55 scripts 4.0k downloads

QuasR - Quantify and Annotate Short Reads in R

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.

Last updated 2 months ago

geneticspreprocessingsequencingchipseqrnaseqmethylseqcoveragealignmentqualitycontrolimmunooncologycurlbzip2xz-utilszlibcpp

8.48 score 5 stars 1 dependents 80 scripts 712 downloads

vsn - Variance stabilization and calibration for microarray data

The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

Last updated 2 months ago

microarrayonechanneltwochannelpreprocessing

8.47 score 50 dependents 856 scripts 7.7k downloads

flowStats - Statistical methods for the analysis of flow cytometry data

Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.

Last updated 2 months ago

immunooncologyflowcytometrycellbasedassays

8.45 score 15 stars 1 dependents 191 scripts 974 downloads

geneplotter - Graphics related functions for Bioconductor

Functions for plotting genomic data

Last updated 2 months ago

visualization

8.43 score 10 dependents 251 scripts 9.0k downloads

POMA - Tools for Omics Data Analysis

The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.

Last updated 25 days ago

batcheffectclassificationclusteringdecisiontreedimensionreductionmultidimensionalscalingnormalizationpreprocessingprincipalcomponentregressionrnaseqsoftwarestatisticalmethodvisualizationbioconductorbioinformaticsdata-visualizationdimension-reductionexploratory-data-analysismachine-learningomics-data-integrationpipelinepre-processingstatistical-analysisuser-friendlyworkflow

8.42 score 11 stars 1 dependents 20 scripts 394 downloads

rawrr - Direct Access to Orbitrap Data and Beyond

This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.

Last updated 18 days ago

massspectrometryproteomicsmetabolomicsinfrastructuresoftwarefastmass-spectrometrymultiplatformorbitrap-ms

8.35 score 54 stars 2 dependents 23 scripts 373 downloads

HIBAG - HLA Genotype Imputation with Attribute Bagging

Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

Last updated 1 months ago

geneticsstatisticalmethodbioinformaticsgpuhlaimputationmhcsnpcpp

8.33 score 30 stars 48 scripts 344 downloads

TRONCO - TRONCO, an R package for TRanslational ONCOlogy

The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).

Last updated 2 months ago

biomedicalinformaticsbayesiangraphandnetworksomaticmutationnetworkinferencenetworkclusteringdataimportsinglecellimmunooncologyalgorithmscancer-inferencetumors

8.33 score 29 stars 38 scripts 254 downloads

piano - Platform for integrative analysis of omics data

Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.

Last updated 2 months ago

microarraypreprocessingqualitycontroldifferentialexpressionvisualizationgeneexpressiongenesetenrichmentpathwaysbioconductorbioconductor-packagebioinformaticsgene-set-enrichmenttranscriptomics

8.30 score 13 stars 7 dependents 182 scripts 796 downloads

gtrellis - Genome Level Trellis Layout

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

Last updated 2 months ago

softwarevisualizationsequencing

8.24 score 39 stars 1 dependents 37 scripts 387 downloads

MSstats - Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.

Last updated 2 months ago

immunooncologymassspectrometryproteomicssoftwarenormalizationqualitycontroltimecourseopenblascpp

8.23 score 6 dependents 157 scripts 836 downloads

STRINGdb - STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis

The STRINGdb package provides a R interface to the STRING protein-protein interactions database (https://string-db.org).

Last updated 2 months ago

network

8.13 score 9 dependents 332 scripts 2.2k downloads

wateRmelon - Illumina DNA methylation array normalization and metrics

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

Last updated 2 months ago

dnamethylationmicroarraytwochannelpreprocessingqualitycontrol

8.11 score 4 dependents 239 scripts 1.5k downloads

ReactomeGSA - Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.

Last updated 24 days ago

genesetenrichmentproteomicstranscriptomicssystemsbiologygeneexpressionreactome

8.06 score 22 stars 48 scripts 382 downloads

Category - Category Analysis

A collection of tools for performing category (gene set enrichment) analysis.

Last updated 2 months ago

annotationgopathwaysgenesetenrichment

8.05 score 19 dependents 204 scripts 2.4k downloads

biovizBase - Basic graphic utilities for visualization of genomic data.

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

Last updated 2 months ago

infrastructurevisualizationpreprocessing

8.05 score 78 dependents 269 scripts 8.9k downloads

siggenes - Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

Last updated 2 months ago

multiplecomparisonmicroarraygeneexpressionsnpexonarraydifferentialexpression

7.95 score 41 dependents 74 scripts 4.9k downloads

MSstatsPTM - Statistical Characterization of Post-translational Modifications

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

Last updated 26 days ago

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolpost-translational-modificationcpp

7.93 score 8 stars 2 dependents 32 scripts 386 downloads

motifStack - Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

Last updated 2 months ago

sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport

7.93 score 6 dependents 189 scripts 1.2k downloads

ChemmineOB - R interface to a subset of OpenBabel functionalities

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

Last updated 2 months ago

cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicsopenbabelcpp

7.88 score 10 stars 1 dependents 76 scripts 1.0k downloads

spicyR - Spatial analysis of in situ cytometry data

The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.

Last updated 1 months ago

singlecellcellbasedassaysspatial

7.88 score 8 stars 1 dependents 41 scripts 350 downloads

beadarray - Quality assessment and low-level analysis for Illumina BeadArray data

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Last updated 2 months ago

microarrayonechannelqualitycontrolpreprocessing

7.86 score 4 dependents 67 scripts 1.1k downloads

COTAN - COexpression Tables ANalysis

Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.

Last updated 1 months ago

systemsbiologytranscriptomicsgeneexpressionsinglecell

7.86 score 15 stars 100 scripts 240 downloads

BiocPkgTools - Collection of simple tools for learning about Bioconductor Packages

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

Last updated 2 months ago

softwareinfrastructurebioconductormetadata

7.85 score 20 stars 68 scripts 485 downloads

mzID - An mzIdentML parser for R

A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.

Last updated 2 months ago

immunooncologydataimportmassspectrometryproteomics

7.82 score 37 dependents 32 scripts 4.7k downloads

Rcpi - Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

Last updated 2 months ago

softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences

7.81 score 37 stars 29 scripts 321 downloads

MGnifyR - R interface to EBI MGnify metagenomics resource

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

Last updated 2 months ago

infrastructuredataimportmetagenomics

7.77 score 19 stars 32 scripts 209 downloads

edge - Extraction of Differential Gene Expression

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as sva and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

Last updated 2 months ago

multiplecomparisondifferentialexpressiontimecourseregressiongeneexpressiondataimport

7.77 score 21 stars 62 scripts 286 downloads

missMethyl - Analysing Illumina HumanMethylation BeadChip Data

Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

Last updated 2 months ago

normalizationdnamethylationmethylationarraygenomicvariationgeneticvariabilitydifferentialmethylationgenesetenrichment

7.74 score 4 dependents 319 scripts 1.8k downloads

gemma.R - A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

Last updated 25 days ago

softwaredataimportmicroarraysinglecellthirdpartyclientdifferentialexpressiongeneexpressionbayesianannotationexperimentaldesignnormalizationbatcheffectpreprocessingbioinformaticsgemmagenomicstranscriptomics

7.71 score 10 stars 26 scripts 214 downloads

FlowSOM - Using self-organizing maps for visualization and interpretation of cytometry data

FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.

Last updated 2 months ago

cellbiologyflowcytometryclusteringvisualizationsoftwarecellbasedassays

7.70 score 10 dependents 470 scripts 1.8k downloads

TSCAN - Tools for Single-Cell Analysis

Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.

Last updated 2 months ago

geneexpressionvisualizationgui

7.66 score 3 dependents 200 scripts 1.0k downloads

DEXSeq - Inference of differential exon usage in RNA-Seq

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Last updated 2 months ago

immunooncologysequencingrnaseqdifferentialexpressionalternativesplicingdifferentialsplicinggeneexpressionvisualization

7.65 score 6 dependents 326 scripts 2.5k downloads

Mfuzz - Soft clustering of omics time series data

The Mfuzz package implements noise-robust soft clustering of omics time-series data, including transcriptomic, proteomic or metabolomic data. It is based on the use of c-means clustering. For convenience, it includes a graphical user interface.

Last updated 2 months ago

microarrayclusteringtimecoursepreprocessingvisualization

7.64 score 4 dependents 336 scripts 2.2k downloads

Heatplus - Heatmaps with row and/or column covariates and colored clusters

Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.

Last updated 2 months ago

microarrayvisualization

7.64 score 5 dependents 96 scripts 901 downloads

MLInterfaces - Uniform interfaces to R machine learning procedures for data in Bioconductor containers

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

Last updated 2 months ago

classificationclustering

7.62 score 6 dependents 78 scripts 878 downloads

openCyto - Hierarchical Gating Pipeline for flow cytometry data

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

Last updated 2 months ago

immunooncologyflowcytometrydataimportpreprocessingdatarepresentationcpp

7.59 score 1 dependents 392 scripts 1.1k downloads

UniProt.ws - R Interface to UniProt Web Services

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases.

Last updated 2 months ago

annotationinfrastructuregokeggbiocartabioconductor-packagecore-package

7.59 score 4 stars 4 dependents 162 scripts 698 downloads

cleaver - Cleavage of Polypeptide Sequences

In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

Last updated 2 months ago

proteomicsbioccleavagedigestpeptides

7.58 score 12 stars 2 dependents 22 scripts 424 downloads

TargetSearch - A package for the analysis of GC-MS metabolite profiling data

This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.

Last updated 1 months ago

massspectrometrypreprocessingdecisiontreeimmunooncologybiocbioconductorgc-msmass-spectrometry

7.53 score 4 stars 3 scripts 270 downloads

ontoProc - processing of ontologies of anatomy, cell lines, and so on

Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

Last updated 17 days ago

infrastructuregobioinformaticsgenomicsontology

7.52 score 3 stars 2 dependents 74 scripts 470 downloads

BUSpaRse - kallisto | bustools R utilities

The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.

Last updated 2 months ago

singlecellrnaseqworkflowstepcpp

7.47 score 9 stars 164 scripts 368 downloads

EBSeq - An R package for gene and isoform differential expression analysis of RNA-seq data

Differential Expression analysis at both gene and isoform level using RNA-seq data

Last updated 2 months ago

immunooncologystatisticalmethoddifferentialexpressionmultiplecomparisonrnaseqsequencing

7.46 score 6 dependents 159 scripts 698 downloads

OrganismDbi - Software to enable the smooth interfacing of different database packages

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

Last updated 2 months ago

annotationinfrastructure

7.45 score 35 dependents 34 scripts 5.3k downloads

flowViz - Visualization for flow cytometry

Provides visualization tools for flow cytometry data.

Last updated 2 months ago

immunooncologyinfrastructureflowcytometrycellbasedassaysvisualization

7.42 score 12 dependents 228 scripts 1.6k downloads

genefu - Computation of Gene Expression-Based Signatures in Breast Cancer

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

Last updated 24 days ago

differentialexpressiongeneexpressionvisualizationclusteringclassification

7.41 score 3 dependents 191 scripts 645 downloads

standR - Spatial transcriptome analyses of Nanostring's DSP data in R

standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

Last updated 20 days ago

spatialtranscriptomicsgeneexpressiondifferentialexpressionqualitycontrolnormalizationexperimenthubsoftware

7.36 score 18 stars 40 scripts 268 downloads

gcrma - Background Adjustment Using Sequence Information

Background adjustment using sequence information

Last updated 2 months ago

microarrayonechannelpreprocessing

7.34 score 12 dependents 164 scripts 1.8k downloads

ncdfFlow - ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.

Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.

Last updated 2 months ago

immunooncologyflowcytometryzlibcpp

7.33 score 11 dependents 92 scripts 1.8k downloads

DSS - Dispersion shrinkage for sequencing data

DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Last updated 2 months ago

sequencingrnaseqdnamethylationgeneexpressiondifferentialexpressiondifferentialmethylation

7.30 score 5 dependents 233 scripts 1.4k downloads

cogena - co-expressed gene-set enrichment analysis

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

Last updated 2 months ago

clusteringgenesetenrichmentgeneexpressionvisualizationpathwayskegggomicroarraysequencingsystemsbiologydatarepresentationdataimportbioconductorbioinformatics

7.22 score 12 stars 23 scripts 232 downloads

mygene - Access MyGene.Info_ services

MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.

Last updated 2 months ago

annotation

7.17 score 1 dependents 330 scripts 571 downloads

mitch - Multi-Contrast Gene Set Enrichment Analysis

mitch is an R package for multi-contrast enrichment analysis. At it’s heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. The rank-MANOVA concept dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). mitch is useful for pathway analysis of profiling studies with one, two or more contrasts, or in studies with multiple omics profiling, for example proteomic, transcriptomic, epigenomic analysis of the same samples. mitch is perfectly suited for pathway level differential analysis of scRNA-seq data. We have an established routine for pathway enrichment of Infinium Methylation Array data (see vignette). The main strengths of mitch are that it can import datasets easily from many upstream tools and has advanced plotting features to visualise these enrichments.

Last updated 26 days ago

geneexpressiongenesetenrichmentsinglecelltranscriptomicsepigeneticsproteomicsdifferentialexpressionreactomednamethylationmethylationarraygene-regulationgene-seq-analysispathway-analysis

7.16 score 16 stars 15 scripts 154 downloads

MsBackendMgf - Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package.

Last updated 1 months ago

infrastructureproteomicsmassspectrometrymetabolomicsdataimport

7.16 score 5 stars 3 dependents 32 scripts 701 downloads

sparrow - Take command of set enrichment analyses through a unified interface

Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

Last updated 19 days ago

genesetenrichmentpathwaysbioinformaticsgsea

7.12 score 21 stars 1 dependents 13 scripts 396 downloads

alabaster.matrix - Load and Save Artifacts from File

Save matrices, arrays and similar objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 19 days ago

dataimportdatarepresentationcpp

7.11 score 8 dependents 13 scripts 3.9k downloads

BiocVersion - Set the appropriate version of Bioconductor packages

This package provides repository information for the appropriate version of Bioconductor.

Last updated 2 months ago

infrastructure

7.10 score 106 dependents 18 scripts 110k downloads

DiffBind - Differential Binding Analysis of ChIP-Seq Peak Data

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Last updated 2 months ago

sequencingchipseqatacseqdnaseseqmethylseqripseqdifferentialpeakcallingdifferentialmethylationgeneregulationhistonemodificationpeakdetectionbiomedicalinformaticscellbiologymultiplecomparisonnormalizationreportwritingepigeneticsfunctionalgenomicscurlbzip2xz-utilszlibcpp

7.08 score 2 dependents 468 scripts 2.1k downloads

ROC - utilities for ROC, with microarray focus

Provide utilities for ROC, with microarray focus.

Last updated 2 months ago

differentialexpression

7.08 score 10 dependents 70 scripts 1.9k downloads

fmcsR - Mismatch Tolerant Maximum Common Substructure Searching

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

Last updated 2 months ago

cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp

7.03 score 5 stars 1 dependents 59 scripts 590 downloads

GOstats - Tools for manipulating GO and microarrays

A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

Last updated 2 months ago

annotationgomultiplecomparisongeneexpressionmicroarraypathwaysgenesetenrichmentgraphandnetwork

7.00 score 14 dependents 516 scripts 2.3k downloads

viper - Virtual Inference of Protein-activity by Enriched Regulon analysis

Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms

Last updated 2 months ago

systemsbiologynetworkenrichmentgeneexpressionfunctionalpredictiongeneregulation

7.00 score 5 dependents 340 scripts 1.1k downloads

BridgeDbR - Code for using BridgeDb identifier mapping framework from within R

Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

Last updated 2 months ago

softwareannotationmetabolomicscheminformaticsbioconductor-packagebridgedbgenesidentifierslife-sciencesmetabolitesproteinsopenjdk

6.97 score 4 stars 43 scripts 230 downloads

RedeR - Interactive visualization and manipulation of nested networks

RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.

Last updated 2 months ago

guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology

6.95 score 7 dependents 107 scripts 540 downloads

cqn - Conditional quantile normalization

A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

Last updated 2 months ago

immunooncologyrnaseqpreprocessingdifferentialexpression

6.94 score 4 dependents 241 scripts 508 downloads

multiGSEA - Combining GSEA-based pathway enrichment with multi omics data integration

Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

Last updated 27 days ago

genesetenrichmentpathwaysreactomebiocarta

6.92 score 17 stars 28 scripts 282 downloads

OncoSimulR - Forward Genetic Simulation of Cancer Progression with Epistasis

Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.

Last updated 2 months ago

biologicalquestionsomaticmutation

6.92 score 6 stars 66 scripts 197 downloads

isobar - Analysis and quantitation of isobarically tagged MSMS proteomics data

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

Last updated 2 months ago

immunooncologyproteomicsmassspectrometrybioinformaticsmultiplecomparisonsqualitycontrol

6.91 score 9 stars 19 scripts 293 downloads

globaltest - Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing

The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Last updated 2 months ago

microarrayonechannelbioinformaticsdifferentialexpressiongopathways

6.91 score 7 dependents 69 scripts 2.8k downloads

RnBeads - RnBeads

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Last updated 2 months ago

dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport

6.90 score 1 dependents 166 scripts 720 downloads

rawDiag - Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.

Last updated 1 months ago

massspectrometryproteomicsmetabolomicsinfrastructuresoftwareshinyappsfastmass-spectrometrymultiplatformorbitrapvisualization

6.89 score 36 stars 18 scripts 152 downloads

SomaticSignatures - Somatic Signatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

Last updated 2 months ago

sequencingsomaticmutationvisualizationclusteringgenomicvariationstatisticalmethod

6.85 score 22 stars 1 dependents 54 scripts 436 downloads

SpotSweeper - Spatially-aware quality control for spatial transcriptomics

Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts.

Last updated 20 days ago

softwarespatialtranscriptomicsqualitycontrolgeneexpressionbioconductorquality-controlspatial-transcriptomics

6.79 score 5 stars 65 scripts 168 downloads

GOexpress - Visualise microarray and RNAseq data using gene ontology annotations

The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.

Last updated 2 months ago

softwaregeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentdatarepresentationclusteringtimecoursemicroarraysequencingrnaseqannotationmultiplecomparisonpathwaysgovisualizationimmunooncologybioconductorbioconductor-packagebioconductor-statsgeneontologygeneset-enrichment

6.75 score 9 stars 31 scripts 250 downloads

mnem - Mixture Nested Effects Models

Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.

Last updated 2 months ago

pathwayssystemsbiologynetworkinferencenetworkrnaseqpooledscreenssinglecellcrispratacseqdnaseqgeneexpressioncpp

6.73 score 4 stars 4 dependents 15 scripts 227 downloads

CellNOptR - Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

Last updated 2 months ago

cellbasedassayscellbiologyproteomicspathwaysnetworktimecourseimmunooncology

6.72 score 6 dependents 98 scripts 318 downloads

bioassayR - Cross-target analysis of small molecule bioactivity

bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.

Last updated 2 months ago

immunooncologymicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportbioinformaticsproteomicsmetabolomics

6.70 score 5 stars 46 scripts 348 downloads

NOISeq - Exploratory analysis and differential expression for RNA-seq data

Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.

Last updated 2 months ago

immunooncologyrnaseqdifferentialexpressionvisualizationsequencing

6.69 score 4 dependents 204 scripts 996 downloads

categoryCompare - Meta-analysis of high-throughput experiments using feature annotations

Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Last updated 2 months ago

annotationgomultiplecomparisonpathwaysgeneexpressionbioconductor

6.68 score 6 stars 252 downloads

kebabs - Kernel-Based Analysis of Biological Sequences

The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.

Last updated 2 months ago

supportvectormachineclassificationclusteringregressioncpp

6.68 score 3 dependents 44 scripts 480 downloads

MotifDb - An Annotated Collection of Protein-DNA Binding Sequence Motifs

More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.

Last updated 2 months ago

motifannotation

6.67 score 2 dependents 390 scripts 982 downloads

ReportingTools - Tools for making reports in various formats

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.

Last updated 2 months ago

immunooncologysoftwarevisualizationmicroarrayrnaseqgodatarepresentationgenesetenrichment

6.65 score 2 dependents 94 scripts 1.1k downloads

pathlinkR - Analyze and interpret RNA-Seq results

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

Last updated 1 months ago

genesetenrichmentnetworkpathwaysreactomernaseqnetworkenrichmentbioinformaticsnetworkspathway-enrichment-analysisvisualization

6.60 score 25 stars 2 scripts 168 downloads

Rbowtie - R bowtie wrapper

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Last updated 2 months ago

sequencingalignment

6.57 score 1 stars 8 dependents 22 scripts 835 downloads

affycoretools - Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

Last updated 2 months ago

reportwritingmicroarrayonechannelgeneexpression

6.56 score 1 dependents 122 scripts 804 downloads

spatialHeatmap - spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.

Last updated 28 days ago

spatialvisualizationmicroarraysequencinggeneexpressiondatarepresentationnetworkclusteringgraphandnetworkcellbasedassaysatacseqdnaseqtissuemicroarraysinglecellcellbiologygenetarget

6.56 score 5 stars 12 scripts 446 downloads

ChAMP - Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

Last updated 2 months ago

microarraymethylationarraynormalizationtwochannelcopynumberdnamethylation

6.55 score 258 scripts 1.4k downloads

APL - Association Plots

APL is a package developed for computation of Association Plots (AP), a method for visualization and analysis of single cell transcriptomics data. The main focus of APL is the identification of genes characteristic for individual clusters of cells from input data. The package performs correspondence analysis (CA) and allows to identify cluster-specific genes using Association Plots. Additionally, APL computes the cluster-specificity scores for all genes which allows to rank the genes by their specificity for a selected cell cluster of interest.

Last updated 2 months ago

statisticalmethoddimensionreductionsinglecellsequencingrnaseqgeneexpression

6.53 score 15 stars 15 scripts 370 downloads

NetPathMiner - NetPathMiner for Biological Network Construction, Path Mining and Visualization

NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.

Last updated 25 days ago

graphandnetworkpathwaysnetworkclusteringclassificationlibsbmllibxml2openblascpp

6.53 score 7 stars 9 scripts 218 downloads

lisaClust - lisaClust: Clustering of Local Indicators of Spatial Association

lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

Last updated 1 months ago

singlecellcellbasedassaysspatial

6.52 score 3 stars 37 scripts 275 downloads

deepSNV - Detection of subclonal SNVs in deep sequencing data.

This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.

Last updated 2 months ago

geneticvariabilitysnpsequencinggeneticsdataimportcurlbzip2xz-utilszlibcpp

6.52 score 1 dependents 37 scripts 506 downloads

lumi - BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

Last updated 2 months ago

microarrayonechannelpreprocessingdnamethylationqualitycontroltwochannel

6.52 score 9 dependents 290 scripts 2.1k downloads

epiregulon - Gene regulatory network inference from single cell epigenomic data

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Last updated 28 days ago

singlecellgeneregulationnetworkinferencenetworkgeneexpressiontranscriptiongenetargetcpp

6.52 score 12 stars 14 scripts 164 downloads

MSstatsTMT - Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Last updated 1 months ago

immunooncologymassspectrometryproteomicssoftware

6.50 score 3 dependents 35 scripts 450 downloads

Rarr - Read Zarr Files in R

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specifcation in R with minimal reliance on an external tools or libraries.

Last updated 27 days ago

dataimportome-zarron-diskout-of-memoryzarrc-blosclibzstd

6.49 score 34 stars 18 scripts 266 downloads

RankProd - Rank Product method for identifying differentially expressed genes with application in meta-analysis

Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification.

Last updated 2 months ago

differentialexpressionstatisticalmethodsoftwareresearchfieldmetabolomicslipidomicsproteomicssystemsbiologygeneexpressionmicroarraygenesignaling

6.48 score 6 dependents 83 scripts 566 downloads

DMRcate - Methylation array and sequencing spatial analysis methods

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

Last updated 2 months ago

differentialmethylationgeneexpressionmicroarraymethylationarraygeneticsdifferentialexpressiongenomeannotationdnamethylationonechanneltwochannelmultiplecomparisonqualitycontroltimecoursesequencingwholegenomeepigeneticscoveragepreprocessingdataimport

6.47 score 1 dependents 302 scripts 1.9k downloads

SPIA - Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.

Last updated 2 months ago

microarraygraphandnetwork

6.46 score 4 dependents 117 scripts 1.0k downloads

Structstrings - Implementation of the dot bracket annotations with Biostrings

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

Last updated 2 months ago

dataimportdatarepresentationinfrastructuresequencingsoftwarealignmentsequencematchingbioconductorrnarna-structural-analysisrna-structuresequencesstructures

6.46 score 4 stars 4 dependents 3 scripts 366 downloads

condiments - Differential Topology, Progression and Differentiation

This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

Last updated 18 days ago

rnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization

6.45 score 25 stars 15 scripts 213 downloads

aroma.light - Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

Last updated 2 months ago

infrastructuremicroarrayonechanneltwochannelmultichannelvisualizationpreprocessingbioconductor

6.44 score 1 stars 20 dependents 26 scripts 2.9k downloads

GeneOverlap - Test and visualize gene overlaps

Test two sets of gene lists and visualize the results.

Last updated 2 months ago

multiplecomparisonvisualization

6.42 score 262 scripts 934 downloads

COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells

COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

Last updated 2 months ago

immunooncologyflowcytometrycpp

6.40 score 6 stars 42 scripts 250 downloads

quantro - A test for when to use quantile normalization

A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

Last updated 2 months ago

normalizationpreprocessingmultiplecomparisonmicroarraysequencing

6.40 score 2 dependents 69 scripts 644 downloads

chipseq - chipseq: A package for analyzing chipseq data

Tools for helping process short read data for chipseq experiments.

Last updated 2 months ago

chipseqsequencingcoveragequalitycontroldataimport

6.39 score 5 dependents 91 scripts 958 downloads

CRISPRseek - Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. The package also output indels and their frequencies for Cas9 targeted sites.

Last updated 2 months ago

immunooncologygeneregulationsequencematchingcrispr

6.36 score 2 dependents 38 scripts 325 downloads

miaViz - Microbiome Analysis Plotting and Visualization

The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.

Last updated 2 months ago

microbiomesoftwarevisualization

6.30 score 1 dependents 79 scripts 486 downloads

BrowserViz - BrowserViz: interactive R/browser graphics using websockets and JSON

Interactvive graphics in a web browser from R, using websockets and JSON.

Last updated 2 months ago

visualizationthirdpartyclient

6.28 score 2 stars 2 dependents 20 scripts 312 downloads

LEA - LEA: an R package for Landscape and Ecological Association Studies

LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.

Last updated 1 months ago

softwarestatistical methodclusteringregressionopenblas

6.27 score 470 scripts 917 downloads

Xeva - Analysis of patient-derived xenograft (PDX) data

The Xeva package provides efficient and powerful functions for patient-drived xenograft (PDX) based pharmacogenomic data analysis. This package contains a set of functions to perform analysis of patient-derived xenograft data. This package was developed by the BHKLab, for further information please see our documentation.

Last updated 24 days ago

geneexpressionpharmacogeneticspharmacogenomicssoftwareclassification

6.26 score 9 stars 17 scripts 332 downloads

gDRstyle - A package with style requirements for the gDR suite

Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met.

Last updated 2 months ago

softwareinfrastructure

6.26 score 2 stars 2 scripts 188 downloads

RMassBank - Workflow to process tandem MS files and build MassBank records

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Last updated 2 months ago

immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk

6.26 score 26 scripts 369 downloads

segmentSeq - Methods for identifying small RNA loci from high-throughput sequencing data

High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.

Last updated 2 months ago

multiplecomparisonsequencingalignmentdifferentialexpressionqualitycontroldataimport

6.25 score 42 scripts 263 downloads

HTSFilter - Filter replicated high-throughput transcriptome sequencing data

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

Last updated 2 months ago

sequencingrnaseqpreprocessingdifferentialexpressiongeneexpressionnormalizationimmunooncology

6.24 score 1 dependents 58 scripts 450 downloads

SynExtend - Tools for Working With Synteny Objects

Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.

Last updated 18 days ago

geneticsclusteringcomparativegenomicsdataimportfortranopenmp

6.23 score 1 stars 70 scripts 160 downloads

SpaceMarkers - Spatial Interaction Markers

Spatial transcriptomic technologies have helped to resolve the connection between gene expression and the 2D orientation of tissues relative to each other. However, the limited single-cell resolution makes it difficult to highlight the most important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software, can help to find molecular interactions, by identifying genes associated with latent space interactions in spatial transcriptomics.

Last updated 2 months ago

singlecellgeneexpressionsoftwarespatialtranscriptomics

6.23 score 4 stars 21 scripts 140 downloads

CNORode - ODE add-on to CellNOptR

Logic based ordinary differential equation (ODE) add-on to CellNOptR.

Last updated 2 months ago

immunooncologycellbasedassayscellbiologyproteomicsbioinformaticstimecourse

6.22 score 1 dependents 37 scripts 250 downloads

qcmetrics - A Framework for Quality Control

The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

Last updated 2 months ago

immunooncologysoftwarequalitycontrolproteomicsmicroarraymassspectrometryvisualizationreportwriting

6.21 score 2 stars 2 dependents 253 downloads

CGHcall - Calling aberrations for array CGH tumor profiles.

Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.

Last updated 2 months ago

microarraypreprocessingvisualization

6.18 score 6 dependents 42 scripts 686 downloads

PROPS - PRObabilistic Pathway Score (PROPS)

This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.

Last updated 25 days ago

classificationbayesiangeneexpression

6.16 score 478 scripts 202 downloads

SAIGEgds - Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies

Scalable implementation of generalized mixed models with highly optimized C++ implementation and integration with Genomic Data Structure (GDS) files. It is designed for single variant tests and set-based aggregate tests in large-scale Phenome-wide Association Studies (PheWAS) with millions of variants and samples, controlling for sample structure and case-control imbalance. The implementation is based on the SAIGE R package (v0.45, Zhou et al. 2018 and Zhou et al. 2020), and it is extended to include the state-of-the-art ACAT-O set-based tests. Benchmarks show that SAIGEgds is significantly faster than the SAIGE R package.

Last updated 1 months ago

softwaregeneticsstatisticalmethodgenomewideassociationgdsgwasmixed-modelphewasopenblascpp

6.15 score 7 stars 15 scripts 254 downloads

sangerseqR - Tools for Sanger Sequencing Data in R

This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

Last updated 2 months ago

sequencingsnpvisualization

6.11 score 2 dependents 64 scripts 1.4k downloads

made4 - Multivariate analysis of microarray data using ADE4

Multivariate data analysis and graphical display of microarray data. Functions include for supervised dimension reduction (between group analysis) and joint dimension reduction of 2 datasets (coinertia analysis). It contains functions that require R package ade4.

Last updated 2 months ago

clusteringclassificationdimensionreductionprincipalcomponenttranscriptomicsmultiplecomparisongeneexpressionsequencingmicroarray

6.10 score 2 dependents 106 scripts 610 downloads

benchdamic - Benchmark of differential abundance methods on microbiome data

Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.

Last updated 26 days ago

metagenomicsmicrobiomedifferentialexpressionmultiplecomparisonnormalizationpreprocessingsoftwarebenchmarkdifferential-abundance-methods

6.09 score 6 stars 23 scripts 216 downloads

CAGEr - Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.

Last updated 2 months ago

preprocessingsequencingnormalizationfunctionalgenomicstranscriptiongeneexpressionclusteringvisualization

6.09 score 69 scripts 564 downloads

gwascat - representing and modeling data in the EMBL-EBI GWAS catalog

Represent and model data in the EMBL-EBI GWAS catalog.

Last updated 2 months ago

genetics

6.08 score 2 dependents 109 scripts 1.2k downloads

mgsa - Model-based gene set analysis

Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.

Last updated 2 months ago

pathwaysgogenesetenrichmentopenmp

6.08 score 5 stars 12 scripts 294 downloads

hopach - Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).

Last updated 2 months ago

clustering

6.05 score 5 dependents 53 scripts 598 downloads

tkWidgets - R based tk widgets

Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.

Last updated 2 months ago

infrastructure

6.05 score 6 dependents 72 scripts 2.1k downloads

synapter - Label-free data analysis pipeline for optimal identification and quantitation

The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.

Last updated 2 months ago

immunooncologymassspectrometryproteomicsqualitycontrol

6.03 score 4 stars 5 scripts 316 downloads

GLAD - Gain and Loss Analysis of DNA

Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

Last updated 2 months ago

microarraycopynumbervariationgslcpp

6.03 score 3 dependents 59 scripts 610 downloads

epialleleR - Fast, Epiallele-Aware Methylation Caller and Reporter

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

Last updated 1 months ago

dnamethylationepigeneticsmethylseqlongreadbioconductordna-methylationepiallelenext-generation-sequencingsamtoolscurlbzip2xz-utilszlibcpp

6.02 score 4 stars 5 scripts 160 downloads

BiocHail - basilisk and hail

Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.

Last updated 1 months ago

infrastructurebioconductorgeneticshail

6.01 score 6 stars 19 scripts 85 downloads

PROcess - Ciphergen SELDI-TOF Processing

A package for processing protein mass spectrometry data.

Last updated 2 months ago

immunooncologymassspectrometryproteomics

6.01 score 512 scripts 304 downloads

autonomics - Unified Statistical Modeling of Omics Data

This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). It provides a fast enrichment analysis implementation. And an intuitive contrastogram visualisation to summarize contrast effects in complex designs.

Last updated 18 days ago

softwaredataimportpreprocessingdimensionreductionprincipalcomponentregressiondifferentialexpressiongenesetenrichmenttranscriptomicstranscriptiongeneexpressionrnaseqmicroarrayproteomicsmetabolomicsmassspectrometry

6.01 score 5 scripts 166 downloads

rpx - R Interface to the ProteomeXchange Repository

The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

Last updated 2 months ago

immunooncologyproteomicsmassspectrometrydataimportthirdpartyclientbioconductordatamass-spectrometryproteomexchange

6.00 score 5 stars 20 scripts 496 downloads

arrayQualityMetrics - Quality metrics report for microarray data sets

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

Last updated 2 months ago

microarrayqualitycontrolonechanneltwochannelreportwriting

5.99 score 1 stars 197 scripts 956 downloads

Rqc - Quality Control Tool for High-Throughput Sequencing Data

Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

Last updated 2 months ago

sequencingqualitycontroldataimportcpp

5.98 score 64 scripts 625 downloads

MsBackendRawFileReader - Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files

implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package.

Last updated 2 months ago

massspectrometryproteomicsmetabolomics

5.94 score 5 stars 5 scripts 212 downloads

ENmix - Quality control and analysis tools for Illumina DNA methylation BeadChip

Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.

Last updated 25 days ago

dnamethylationpreprocessingqualitycontroltwochannelmicroarrayonechannelmethylationarraybatcheffectnormalizationdataimportregressionprincipalcomponentepigeneticsmultichanneldifferentialmethylationimmunooncology

5.93 score 106 scripts 627 downloads

cummeRbund - Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

Last updated 2 months ago

highthroughputsequencinghighthroughputsequencingdatarnaseqrnaseqdatageneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationbioinformaticsclusteringmultiplecomparisonsqualitycontrol

5.92 score 209 scripts 592 downloads

fastseg - fastseg - a fast segmentation algorithm

fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments.

Last updated 30 days ago

classificationcopynumbervariation

5.90 score 4 dependents 20 scripts 1.2k downloads

BEclear - Correction of batch effects in DNA methylation data

Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Last updated 2 months ago

batcheffectdnamethylationsoftwarepreprocessingstatisticalmethodbatch-effectsbioconductor-packagedna-methylationlatent-factor-modelmethylationmissing-datamissing-valuesstochastic-gradient-descentcpp

5.90 score 4 stars 11 scripts 324 downloads

SGSeq - Splice event prediction and quantification from RNA-seq data

SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.

Last updated 2 months ago

alternativesplicingimmunooncologyrnaseqtranscription

5.90 score 3 dependents 44 scripts 669 downloads

oligoClasses - Classes for high-throughput arrays supported by oligo and crlmm

This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

Last updated 2 months ago

infrastructure

5.90 score 19 dependents 93 scripts 2.5k downloads

Repitools - Epigenomic tools

Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

Last updated 2 months ago

dnamethylationgeneexpressionmethylseq

5.90 score 263 scripts 525 downloads

HMMcopy - Copy number prediction with correction for GC and mappability bias for HTS data

Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.

Last updated 2 months ago

sequencingpreprocessingvisualizationcopynumbervariationmicroarray

5.89 score 1 dependents 129 scripts 633 downloads

bioDist - Different distance measures

A collection of software tools for calculating distance measures.

Last updated 2 months ago

clusteringclassification

5.86 score 2 dependents 61 scripts 568 downloads

flowPeaks - An R package for flow data clustering

A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

Last updated 30 days ago

immunooncologyflowcytometryclusteringgatinggslcpp

5.86 score 2 dependents 30 scripts 336 downloads

affycomp - Graphics Toolbox for Assessment of Affymetrix Expression Measures

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.

Last updated 2 months ago

onechannelmicroarraypreprocessing

5.86 score 12 scripts 452 downloads

rBiopaxParser - Parses BioPax files and represents them in R

Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

Last updated 2 months ago

datarepresentation

5.85 score 10 stars 7 scripts 356 downloads

GBScleanR - Error correction tool for noisy genotyping by sequencing (GBS) data

GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.

Last updated 2 months ago

geneticvariabilitysnpgeneticshiddenmarkovmodelsequencingqualitycontrolcpp

5.83 score 4 stars 6 scripts 206 downloads

RTN - RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

Last updated 2 months ago

transcriptionnetworknetworkinferencenetworkenrichmentgeneregulationgeneexpressiongraphandnetworkgenesetenrichmentgeneticvariability

5.81 score 2 dependents 54 scripts 356 downloads

scRNAseqApp - A single-cell RNAseq Shiny app-package

The scRNAseqApp is a Shiny app package designed for interactive visualization of single-cell data. It is an enhanced version derived from the ShinyCell, repackaged to accommodate multiple datasets. The app enables users to visualize data containing various types of information simultaneously, facilitating comprehensive analysis. Additionally, it includes a user management system to regulate database accessibility for different users.

Last updated 1 months ago

visualizationsinglecellrnaseqinteractive-visualizationsmultiple-usersshiny-appssingle-cell-rna-seq

5.79 score 4 stars 3 scripts 158 downloads

safe - Significance Analysis of Function and Expression

SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.

Last updated 2 months ago

differentialexpressionpathwaysgenesetenrichmentstatisticalmethodsoftware

5.78 score 5 dependents 49 scripts 1.0k downloads

RPA - RPA: Robust Probabilistic Averaging for probe-level analysis

Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.

Last updated 2 months ago

geneexpressionmicroarraypreprocessingqualitycontrol

5.78 score 1 dependents 20 scripts 300 downloads

iClusterPlus - Integrative clustering of multi-type genomic data

Integrative clustering of multiple genomic data using a joint latent variable model.

Last updated 29 days ago

multi-omicsclustering

5.75 score 188 scripts 846 downloads

quantsmooth - Quantile smoothing and genomic visualization of array data

Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.

Last updated 2 months ago

visualizationcopynumbervariation

5.73 score 7 dependents 40 scripts 1.1k downloads

ASSET - An R package for subset-based association analysis of heterogeneous traits and subtypes

An R package for subset-based analysis of heterogeneous traits and disease subtypes. The package allows the user to search through all possible subsets of z-scores to identify the subset of traits giving the best meta-analyzed z-score. Further, it returns a p-value adjusting for the multiple-testing involved in the search. It also allows for searching for the best combination of disease subtypes associated with each variant.

Last updated 2 months ago

statisticalmethodsnpgenomewideassociationmultiplecomparison

5.70 score 1 dependents 83 scripts 352 downloads

AnVILGCP - The GCP R Client for the AnVIL

The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to work with the AnVIL package. User-level interaction with this package should be minimal.

Last updated 2 months ago

softwareinfrastructurethirdpartyclientdataimport

5.67 score 3 dependents 25 scripts 93 downloads

hpar - Human Protein Atlas in R

The hpar package provides a simple R interface to and data from the Human Protein Atlas project.

Last updated 2 months ago

proteomicscellbiologydataimportfunctionalgenomicssystemsbiologyexperimenthubsoftware

5.67 score 1 dependents 31 scripts 728 downloads

pvca - Principal Variance Component Analysis (PVCA)

This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.

Last updated 2 months ago

microarraybatcheffect

5.66 score 1 dependents 110 scripts 514 downloads

sangeranalyseR - sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

Last updated 2 months ago

geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationgui

5.66 score 46 scripts 393 downloads

cn.mops - cn.mops - Mixture of Poissons for CNV detection in NGS data

cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.

Last updated 2 months ago

sequencingcopynumbervariationhomo_sapienscellbiologyhapmapgeneticscpp

5.65 score 4 dependents 94 scripts 444 downloads

multicrispr - Multi-locus multi-purpose Crispr/Cas design

This package is for designing Crispr/Cas9 and Prime Editing experiments. It contains functions to (1) define and transform genomic targets, (2) find spacers (4) count offtarget (mis)matches, and (5) compute Doench2016/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets, enabling the design of large Crispr/Cas9 libraries.

Last updated 25 days ago

crisprsoftware

5.65 score 2 scripts 175 downloads

BindingSiteFinder - Binding site defintion based on iCLIP data

Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

Last updated 1 months ago

sequencinggeneexpressiongeneregulationfunctionalgenomicscoveragedataimportbinding-site-classificationbinding-sitesbioconductor-packageicliprna-binding-proteins

5.65 score 6 stars 3 scripts 158 downloads

annaffy - Annotation tools for Affymetrix biological metadata

Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.

Last updated 2 months ago

onechannelmicroarrayannotationgopathwaysreportwriting

5.64 score 3 dependents 60 scripts 720 downloads

rcellminer - rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

Last updated 2 months ago

acghcellbasedassayscopynumbervariationgeneexpressionpharmacogenomicspharmacogeneticsmirnacheminformaticsvisualizationsoftwaresystemsbiology

5.63 score 95 scripts 246 downloads

qusage - qusage: Quantitative Set Analysis for Gene Expression

This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. The QuSAGE package also includes a mixed effects model implementation, as described in (Turner JA et al, BMC Bioinformatics, 2015), and a meta-analysis framework as described in (Meng H, et al. PLoS Comput Biol. 2019). For questions, contact Chris Bolen ([email protected]) or Steven Kleinstein ([email protected])

Last updated 2 months ago

genesetenrichmentmicroarrayrnaseqsoftwareimmunooncology

5.63 score 1 dependents 177 scripts 665 downloads

TENxIO - Import methods for 10X Genomics files

Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.

Last updated 30 days ago

softwareinfrastructuredataimportsinglecellbioconductor-package

5.62 score 2 dependents 7 scripts 110 downloads

similaRpeak - Metrics to estimate a level of similarity between two ChIP-Seq profiles

This package calculates metrics which quantify the level of similarity between ChIP-Seq profiles. More specifically, the package implements six pseudometrics specialized in pattern similarity detection in ChIP-Seq profiles.

Last updated 2 months ago

biologicalquestionchipseqgeneticsmultiplecomparisondifferentialexpressionbioconductorbioconductor-packagechip-profileschip-seqmetrics

5.62 score 7 stars 7 scripts 240 downloads

R3CPET - 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.

Last updated 2 months ago

networkinferencegenepredictionbayesiangraphandnetworknetworkgeneexpressionhicchia-petchromatin-interactiondirichlet-process-mixturestranscription-facto

5.62 score 4 stars 5 scripts 196 downloads

makecdfenv - CDF Environment Maker

This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.

Last updated 2 months ago

onechanneldataimportpreprocessingzlib

5.62 score 2 dependents 35 scripts 544 downloads

genomeIntervals - Operations on genomic intervals

This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'.

Last updated 2 months ago

dataimportinfrastructuregenetics

5.61 score 3 dependents 45 scripts 386 downloads

convert - Convert Microarray Data Objects

Define coerce methods for microarray data objects.

Last updated 2 months ago

infrastructuremicroarraytwochannel

5.58 score 1 dependents 91 scripts 397 downloads

seqTools - Analysis of nucleotide, sequence and quality content on fastq files

Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.

Last updated 2 months ago

qualitycontrolsequencingzlib

5.57 score 1 dependents 52 scripts 275 downloads

ctc - Cluster and Tree Conversion.

Tools for export and import classification trees and clusters to other programs

Last updated 2 months ago

microarrayclusteringclassificationdataimportvisualization

5.57 score 2 dependents 62 scripts 588 downloads

EBarrays - Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification

EBarrays provides tools for the analysis of replicated/unreplicated microarray data.

Last updated 2 months ago

clusteringdifferentialexpression

5.56 score 6 dependents 5 scripts 550 downloads

gDR - Umbrella package for R packages in the gDR suite

Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.

Last updated 2 months ago

softwaredataimportshinyapps

5.56 score 1 stars 7 scripts 106 downloads

VanillaICE - A Hidden Markov Model for high throughput genotyping arrays

Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays.

Last updated 2 months ago

copynumbervariation

5.53 score 1 dependents 63 scripts 504 downloads

GenomicTuples - Representation and Manipulation of Genomic Tuples

GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

Last updated 1 months ago

infrastructuredatarepresentationsequencingcpp

5.48 score 4 stars 7 scripts 216 downloads

bandle - An R package for the Bayesian analysis of differential subcellular localisation experiments

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

Last updated 2 months ago

bayesianclassificationclusteringimmunooncologyqualitycontroldataimportproteomicsmassspectrometryopenblascppopenmp

5.48 score 5 stars 3 scripts 137 downloads

tilingArray - Transcript mapping with high-density oligonucleotide tiling arrays

The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.

Last updated 2 months ago

microarrayonechannelpreprocessingvisualization

5.48 score 1 dependents 5 scripts 457 downloads

omicade4 - Multiple co-inertia analysis of omics datasets

This package performes multiple co-inertia analysis of omics datasets.

Last updated 2 months ago

softwareclusteringclassificationmultiplecomparison

5.47 score 1 dependents 49 scripts 444 downloads

conumee - Enhanced copy-number variation analysis using Illumina DNA methylation arrays

This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.

Last updated 2 months ago

copynumbervariationdnamethylationmethylationarraymicroarraynormalizationpreprocessingqualitycontrolsoftware

5.46 score 29 scripts 404 downloads

specL - specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>.

Last updated 2 months ago

massspectrometryproteomicsddadiamass-spectrometry

5.46 score 1 stars 12 scripts 248 downloads

CleanUpRNAseq - Detect and Correct Genomic DNA Contamination in RNA-seq Data

RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.

Last updated 1 months ago

qualitycontrolsequencinggeneexpression

5.44 score 5 stars 4 scripts 124 downloads

iPAC - Identification of Protein Amino acid Clustering

iPAC is a novel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure.

Last updated 2 months ago

clusteringproteomics

5.43 score 3 dependents 3 scripts 244 downloads

easyRNASeq - Count summarization and normalization for RNA-Seq data

Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.

Last updated 2 months ago

geneexpressionrnaseqgeneticspreprocessingimmunooncology

5.43 score 1 dependents 15 scripts 402 downloads

HiTC - High Throughput Chromosome Conformation Capture analysis

The HiTC package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.

Last updated 2 months ago

sequencinghighthroughputsequencinghic

5.40 score 42 scripts 462 downloads

TCC - TCC: Differential expression analysis for tag count data with robust normalization strategies

This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.

Last updated 2 months ago

immunooncologysequencingdifferentialexpressionrnaseq

5.40 score 42 scripts 504 downloads

iSEEde - iSEE extension for panels related to differential expression analysis

This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

Last updated 2 months ago

softwareinfrastructuredifferentialexpressionbioconductorhacktoberfestiseeu

5.38 score 1 stars 15 scripts 137 downloads

bettr - A Better Way To Explore What Is Best

bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations.

Last updated 2 months ago

visualizationshinyappsgui

5.38 score 3 stars 3 scripts 124 downloads

AIMS - AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.

Last updated 2 months ago

immunooncologyclassificationrnaseqmicroarraysoftwaregeneexpression

5.38 score 4 dependents 10 scripts 724 downloads

aCGH - Classes and functions for Array Comparative Genomic Hybridization data

Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

Last updated 2 months ago

copynumbervariationdataimportgeneticscpp

5.38 score 4 dependents 9 scripts 536 downloads

MsBackendSql - SQL-based Mass Spectrometry Data Backend

SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.

Last updated 1 months ago

infrastructuremassspectrometrymetabolomicsdataimportproteomics

5.35 score 4 stars 16 scripts 160 downloads

CODEX - A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.

Last updated 2 months ago

immunooncologyexomeseqnormalizationqualitycontrolcopynumbervariation

5.33 score 1 dependents 36 scripts 250 downloads

eiR - Accelerated similarity searching of small molecules

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Last updated 2 months ago

cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomics

5.33 score 3 stars 12 scripts 250 downloads

SCArray - Large-scale single-cell omics data manipulation with GDS files

Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.

Last updated 1 months ago

infrastructuredatarepresentationdataimportsinglecellrnaseqcpp

5.32 score 1 stars 1 dependents 9 scripts 188 downloads

nucleR - Nucleosome positioning package for R

Nucleosome positioning for Tiling Arrays and NGS experiments.

Last updated 2 months ago

nucleosomepositioningcoveragechipseqmicroarraysequencinggeneticsqualitycontroldataimport

5.32 score 21 scripts 293 downloads

GlobalAncova - Global test for groups of variables via model comparisons

The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.

Last updated 2 months ago

microarrayonechanneldifferentialexpressionpathwaysregression

5.32 score 1 dependents 9 scripts 1.7k downloads

fobitools - Tools for Manipulating the FOBI Ontology

A set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.

Last updated 24 days ago

massspectrometrymetabolomicssoftwarevisualizationbiomedicalinformaticsgraphandnetworkannotationcheminformaticspathwaysgenesetenrichmentbiological-intrerpretationbiological-knowledgebiological-significance-analysisenrichment-analysisfood-biomarker-ontologyknowledge-graphnutritionobofoundryontologytext-mining

5.30 score 1 stars 5 scripts 187 downloads

PADOG - Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.

Last updated 2 months ago

microarrayonechanneltwochannel

5.30 score 2 dependents 11 scripts 550 downloads

CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses.

This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data

Last updated 2 months ago

microarraycopynumbervariation

5.30 score 1 dependents 33 scripts 320 downloads

SplicingGraphs - Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.

Last updated 2 months ago

geneticsannotationdatarepresentationvisualizationsequencingrnaseqgeneexpressionalternativesplicingtranscriptionimmunooncologybioconductor-package

5.26 score 2 stars 8 scripts 282 downloads

canceR - A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

Last updated 2 months ago

guigeneexpressionclusteringgogenesetenrichmentkeggmultiplecomparisoncancercancer-datagenegene-expressiongene-methylationgene-mutationgene-setsmethylationmskccmutationstcltk

5.25 score 7 stars 17 scripts 261 downloads

epivizr - R Interface to epiviz web app

This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.

Last updated 2 months ago

visualizationinfrastructuregui

5.24 score 2 dependents 29 scripts 280 downloads

muscle - Multiple Sequence Alignment with MUSCLE

MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.

Last updated 2 months ago

multiplesequencealignmentalignmentsequencinggeneticssequencematchingdataimportcpp

5.21 score 81 scripts 564 downloads

OmicCircos - High-quality circular visualization of omics data

OmicCircos is an R application and package for generating high-quality circular plots for omics data.

Last updated 2 months ago

visualizationstatisticsannotation

5.20 score 79 scripts 337 downloads

maSigPro - Significant Gene Expression Profile Differences in Time Course Gene Expression Data

maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.

Last updated 2 months ago

microarrayrna-seqdifferential expressiontimecourse

5.19 score 78 scripts 598 downloads

groHMM - GRO-seq Analysis Pipeline

A pipeline for the analysis of GRO-seq data.

Last updated 18 days ago

sequencingsoftware

5.18 score 1 stars 25 scripts 328 downloads

MEDIPS - DNA IP-seq data analysis

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.

Last updated 2 months ago

dnamethylationcpgislanddifferentialexpressionsequencingchipseqpreprocessingqualitycontrolvisualizationmicroarraygeneticscoveragegenomeannotationcopynumbervariationsequencematching

5.17 score 74 scripts 346 downloads

DeconRNASeq - Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data

DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

Last updated 2 months ago

differentialexpression

5.16 score 72 scripts 612 downloads

BERT - High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)

Provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Last updated 1 months ago

batcheffectpreprocessingexperimentaldesignqualitycontrol

5.13 score 2 stars 17 scripts 110 downloads

BRAIN - Baffling Recursive Algorithm for Isotope distributioN calculations

Package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm described in the paper by J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg.

Last updated 2 months ago

immunooncologymassspectrometryproteomics

5.11 score 13 scripts 328 downloads

ROntoTools - R Onto-Tools suite

Suite of tools for functional analysis.

Last updated 2 months ago

networkanalysismicroarraygraphsandnetworks

5.10 score 2 dependents 15 scripts 364 downloads

MANOR - CGH Micro-Array NORmalization

Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.

Last updated 2 months ago

microarraytwochanneldataimportqualitycontrolpreprocessingcopynumbervariationnormalization

5.10 score 1 scripts 390 downloads

GreyListChIP - Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.

Last updated 2 months ago

chipseqalignmentpreprocessingdifferentialpeakcallingsequencinggenomeannotationcoverage

5.10 score 4 dependents 9 scripts 1.7k downloads

alabaster.spatial - Save and Load Spatial 'Omics Data to/from File

Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Last updated 1 months ago

dataimportdatarepresentation

5.08 score 1 dependents 5 scripts 172 downloads

PROPER - PROspective Power Evaluation for RNAseq

This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.

Last updated 2 months ago

immunooncologysequencingrnaseqdifferentialexpression

5.08 score 1 dependents 20 scripts 268 downloads

AllelicImbalance - Investigates Allele Specific Expression

Provides a framework for allelic specific expression investigation using RNA-seq data.

Last updated 2 months ago

geneticsinfrastructuresequencing

5.08 score 6 scripts 391 downloads

pathifier - Quantify deregulation of pathways in cancer

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

Last updated 2 months ago

network

5.07 score 1 dependents 28 scripts 214 downloads

spoon - Address the Mean-variance Relationship in Spatial Transcriptomics Data

This package addresses the mean-variance relationship in spatially resolved transcriptomics data. Precision weights are generated for individual observations using Empirical Bayes techniques. These weights are used to rescale the data and covariates, which are then used as input in spatially variable gene detection tools.

Last updated 1 months ago

spatialsinglecelltranscriptomicsgeneexpressionpreprocessing

5.07 score 18 scripts 124 downloads

MSnID - Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

Last updated 2 months ago

proteomicsmassspectrometryimmunooncology

5.06 score 57 scripts 635 downloads

PWMEnrich - PWM enrichment analysis

A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.

Last updated 2 months ago

motifannotationsequencematchingsoftware

5.06 score 57 scripts 397 downloads

roar - Identify differential APA usage from RNA-seq alignments

Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.

Last updated 2 months ago

sequencinghighthroughputsequencingrnaseqtranscription

5.05 score 4 stars 14 scripts 359 downloads

widgetTools - Creates an interactive tcltk widget

This packages contains tools to support the construction of tcltk widgets

Last updated 2 months ago

infrastructure

5.04 score 8 dependents 11 scripts 2.1k downloads

msmsTests - LC-MS/MS Differential Expression Tests

Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

Last updated 2 months ago

immunooncologysoftwaremassspectrometryproteomics

5.03 score 1 dependents 15 scripts 595 downloads

DEGseq - Identify Differentially Expressed Genes from RNA-seq data

DEGseq is an R package to identify differentially expressed genes from RNA-Seq data.

Last updated 2 months ago

rnaseqpreprocessinggeneexpressiondifferentialexpressionimmunooncologycpp

5.03 score 54 scripts 340 downloads

MSA2dist - MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.

Last updated 1 months ago

alignmentsequencinggeneticsgocpp

5.02 score 1 dependents 7 scripts 256 downloads

podkat - Position-Dependent Kernel Association Test

This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

Last updated 2 months ago

geneticswholegenomeannotationvariantannotationsequencingdataimportcurlbzip2xz-utilszlibcpp

5.02 score 6 scripts 236 downloads

casper - Characterization of Alternative Splicing based on Paired-End Reads

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Last updated 1 months ago

immunooncologygeneexpressiondifferentialexpressiontranscriptionrnaseqsequencing

5.02 score 65 scripts 252 downloads

ReadqPCR - Read qPCR data

The package provides functions to read raw RT-qPCR data of different platforms.

Last updated 2 months ago

dataimportmicrotitreplateassaygeneexpressionqpcr

5.01 score 1 dependents 17 scripts 367 downloads

PolySTest - PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values

The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.

Last updated 30 days ago

massspectrometryproteomicssoftwaredifferentialexpression

5.00 score 10 scripts 46 downloads

geomeTriD - A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data

geomeTriD (Three Dimensional Geometry Package) create interactive 3D plots using the GL library with the 'three.js' visualization library (https://threejs.org) or the rgl library. In addition to creating interactive 3D plots, the application also generates simplified models in 2D. These 2D models provide a more straightforward visual representation, making it easier to analyze and interpret the data quickly. This functionality ensures that users have access to both detailed three-dimensional visualizations and more accessible two-dimensional views, catering to various analytical needs.

Last updated 1 months ago

visualization

5.00 score 1 stars 7 scripts 74 downloads

GSCA - GSCA: Gene Set Context Analysis

GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.

Last updated 2 months ago

geneexpressionvisualizationgui

5.00 score 5 scripts 210 downloads

GeneExpressionSignature - Gene Expression Signature based Similarity Metric

This package gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

Last updated 2 months ago

geneexpression

5.00 score 1 stars 4 scripts 280 downloads

TPP - Analyze thermal proteome profiling (TPP) experiments

Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).

Last updated 2 months ago

immunooncologyproteomicsmassspectrometry

4.98 score 16 scripts 270 downloads

sSeq - Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.

Last updated 2 months ago

immunooncologyrnaseq

4.98 score 2 dependents 4 scripts 308 downloads

mspms - Tools for the analysis of MSP-MS data

This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.

Last updated 19 days ago

proteomicsmassspectrometrypreprocessingproteaseproteomics-data-analysis

4.95 score 4 scripts

SplineDV - Differential Variability (DV) analysis for single-cell RNA sequencing data. (e.g. Identify Differentially Variable Genes across two experimental conditions)

A spline based scRNA-seq method for identifying differentially variable (DV) genes across two experimental conditions. Spline-DV constructs a 3D spline from 3 key gene statistics: mean expression, coefficient of variance, and dropout rate. This is done for both conditions. The 3D spline provides the “expected” behavior of genes in each condition. The distance of the observed mean, CV and dropout rate of each gene from the expected 3D spline is used to measure variability. As the final step, the spline-DV method compares the variabilities of each condition to identify differentially variable (DV) genes.

Last updated 1 months ago

softwaresinglecellsequencingdifferentialexpressionrnaseqgeneexpressiontranscriptomicsfeatureextraction

4.95 score 2 stars 3 scripts

RRHO - Inference on agreement between ordered lists

The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.

Last updated 2 months ago

geneticssequencematchingmicroarraytranscription

4.95 score 45 scripts 216 downloads

procoil - Prediction of Oligomerization of Coiled Coil Proteins

The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.

Last updated 2 months ago

proteomicsclassificationsupportvectormachine

4.95 score 1 scripts 434 downloads

altcdfenvs - alternative CDF environments (aka probeset mappings)

Convenience data structures and functions to handle cdfenvs

Last updated 2 months ago

microarrayonechannelqualitycontrolpreprocessingannotationproprietaryplatformstranscription

4.95 score 1 dependents 5 scripts 432 downloads

miRNAtap - miRNAtap: microRNA Targets - Aggregated Predictions

The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).

Last updated 2 months ago

softwareclassificationmicroarraysequencingmirna

4.93 score 43 scripts 337 downloads

ginmappeR - Gene Identifier Mapper

Provides functionalities to translate gene or protein identifiers between state-of-art biological databases: CARD (<https://card.mcmaster.ca/>), NCBI Protein, Nucleotide and Gene (<https://www.ncbi.nlm.nih.gov/>), UniProt (<https://www.uniprot.org/>) and KEGG (<https://www.kegg.jp>). Also offers complementary functionality like NCBI identical proteins or UniProt similar genes clusters retrieval.

Last updated 19 days ago

annotationkegggeneticsthirdpartyclientsoftware

4.93 score 7 scripts 156 downloads

GeneNetworkBuilder - GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

Last updated 2 months ago

sequencingmicroarraygraphandnetworkcpp

4.93 score 17 scripts 272 downloads

CNVrd2 - CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

Last updated 2 months ago

copynumbervariationsnpsequencingsoftwarecoveragelinkagedisequilibriumclustering.jagscpp

4.92 score 3 stars 230 downloads

gmapR - An R interface to the GMAP/GSNAP/GSTRUCT suite

GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.

Last updated 2 months ago

alignmentzlib

4.91 score 1 dependents 45 scripts 360 downloads

tweeDEseq - RNA-seq data analysis using the Poisson-Tweedie family of distributions

Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.

Last updated 2 months ago

immunooncologystatisticalmethoddifferentialexpressionsequencingrnaseqdnaseq

4.91 score 1 dependents 45 scripts 354 downloads

motifTestR - Perform key tests for binding motifs in sequence data

Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.

Last updated 2 months ago

motifannotationchipseqchiponchipsequencematchingsoftware

4.90 score 1 stars 2 scripts 180 downloads

immApex - Tools for Adaptive Immune Receptor Sequence-Based Keras Modeling

A set of tools to build tensorflow/keras3-based models in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.

Last updated 2 months ago

softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotation

4.88 score 8 stars 4 scripts

beachmat.hdf5 - beachmat bindings for HDF5-backed matrices

Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

Last updated 1 months ago

datarepresentationdataimportinfrastructurezlibcpp

4.88 score 6 scripts 244 downloads

AnVILWorkflow - Run workflows implemented in Terra/AnVIL workspace

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.

Last updated 2 months ago

infrastructuresoftwareanvilgcpterraworkflows

4.88 score 5 stars 1 scripts 112 downloads

rTRM - Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks

rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

Last updated 2 months ago

transcriptionnetworkgeneregulationgraphandnetworkbioconductorbioinformatics

4.86 score 3 stars 1 dependents 3 scripts 305 downloads

csdR - Differential gene co-expression

This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford's algorithm.

Last updated 2 months ago

differentialexpressiongraphandnetworkgeneexpressionnetworkcppopenmp

4.85 score 7 stars 7 scripts 120 downloads

MethylSeekR - Segmentation of Bis-seq data

This is a package for the discovery of regulatory regions from Bis-seq data

Last updated 2 months ago

sequencingmethylseqdnamethylation

4.83 score 34 scripts 395 downloads

MLSeq - Machine Learning Interface for RNA-Seq Data

This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data.

Last updated 2 months ago

immunooncologysequencingrnaseqclassificationclustering

4.80 score 1 dependents 26 scripts 306 downloads

HoloFoodR - R interface to EBI HoloFood resource

Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.

Last updated 2 months ago

softwareinfrastructuredataimport

4.78 score 1 stars 6 scripts 65 downloads

IVAS - Identification of genetic Variants affecting Alternative Splicing

Identification of genetic variants affecting alternative splicing.

Last updated 2 months ago

immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressiongeneregulationregressionrnaseqsequencingsnpsoftwaretranscription

4.78 score 1 dependents 1 scripts 230 downloads

BiSeq - Processing and analyzing bisulfite sequencing data

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

Last updated 2 months ago

geneticssequencingmethylseqdnamethylation

4.78 score 30 scripts 303 downloads

SPEM - S-system parameter estimation method

This package can optimize the parameter in S-system models given time series data

Last updated 2 months ago

networknetworkinferencesoftware

4.78 score 1 dependents 4 scripts 263 downloads

DTA - Dynamic Transcriptome Analysis

Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements.

Last updated 2 months ago

microarraydifferentialexpressiongeneexpressiontranscription

4.78 score 1 dependents 8 scripts 220 downloads

MLP - Mean Log P Analysis

Pathway analysis based on p-values associated to genes from a genes expression analysis of interest. Utility functions enable to extract pathways from the Gene Ontology Biological Process (GOBP), Molecular Function (GOMF) and Cellular Component (GOCC), Kyoto Encyclopedia of Genes of Genomes (KEGG) and Reactome databases. Methodology, and helper functions to display the results as a table, barplot of pathway significance, Gene Ontology graph and pathway significance are available.

Last updated 2 months ago

geneticsgeneexpressionpathwaysreactomekegggo

4.78 score 1 dependents 4 scripts 312 downloads

GeneMeta - MetaAnalysis for High Throughput Experiments

A collection of meta-analysis tools for analysing high throughput experimental data

Last updated 2 months ago

sequencinggeneexpressionmicroarray

4.78 score 1 dependents 2 scripts 360 downloads

OLIN - Optimized local intensity-dependent normalisation of two-color microarrays

Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data

Last updated 2 months ago

microarraytwochannelqualitycontrolpreprocessingvisualization

4.78 score 1 dependents 2 scripts 335 downloads

seqPattern - Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences

Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

Last updated 2 months ago

visualizationsequencematching

4.77 score 7 dependents 12 scripts 1.2k downloads

chipenrich - Gene Set Enrichment For ChIP-seq Peak Data

ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

Last updated 2 months ago

immunooncologychipseqepigeneticsfunctionalgenomicsgenesetenrichmenthistonemodificationregression

4.76 score 29 scripts 304 downloads

TFutils - TFutils

This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.

Last updated 1 months ago

transcriptomics

4.76 score 19 scripts 236 downloads

Summix - Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data

This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data.

Last updated 1 months ago

statisticalmethodwholegenomegenetics

4.75 score 14 scripts 170 downloads

EnrichDO - a Global Weighted Model for Disease Ontology Enrichment Analysis

To implement disease ontology (DO) enrichment analysis, this package is designed and presents a double weighted model based on the latest annotations of the human genome with DO terms, by integrating the DO graph topology on a global scale. This package exhibits high accuracy that it can identify more specific DO terms, which alleviates the over enriched problem. The package includes various statistical models and visualization schemes for discovering the associations between genes and diseases from biological big data.

Last updated 24 days ago

annotationvisualizationgenesetenrichmentsoftware

4.74 score 7 scripts

methylPipe - Base resolution DNA methylation data analysis

Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.

Last updated 2 months ago

methylseqdnamethylationcoveragesequencing

4.73 score 1 dependents 1 scripts 273 downloads

RNASeqPower - Sample size for RNAseq studies

RNA-seq, sample size

Last updated 2 months ago

immunooncologyrnaseq

4.73 score 27 scripts 326 downloads

flowFP - Fingerprinting for Flow Cytometry

Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

Last updated 2 months ago

flowcytometrycellbasedassaysclusteringvisualization

4.72 score 2 dependents 11 scripts 342 downloads

customProDB - Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.

Last updated 2 months ago

immunooncologysequencingmassspectrometryproteomicssnprnaseqsoftwaretranscriptionalternativesplicingfunctionalgenomics

4.72 score 15 scripts 250 downloads

frma - Frozen RMA and Barcode

Preprocessing and analysis for single microarrays and microarray batches.

Last updated 2 months ago

softwaremicroarraypreprocessing

4.72 score 1 dependents 87 scripts 360 downloads

interactiveDisplayBase - Base package for enabling powerful shiny web displays of Bioconductor objects

The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.

Last updated 2 months ago

gogeneexpressionmicroarraysequencingclassificationnetworkqualitycontrolvisualizationgeneticsdatarepresentationguiannotationdatashinyapps

4.72 score 1 dependents 5 scripts 8.7k downloads

MethylMix - MethylMix: Identifying methylation driven cancer genes

MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.

Last updated 2 months ago

dnamethylationstatisticalmethoddifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetwork

4.72 score 26 scripts 284 downloads

NormqPCR - Functions for normalisation of RT-qPCR data

Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.

Last updated 2 months ago

microtitreplateassaygeneexpressionqpcr

4.72 score 26 scripts 358 downloads

SBMLR - SBML-R Interface and Analysis Tools

This package contains a systems biology markup language (SBML) interface to R.

Last updated 2 months ago

graphandnetworkpathwaysnetwork

4.71 score 43 scripts 300 downloads

rSWeeP - Spaced Words Projection (SWeeP)

"Spaced Words Projection (SWeeP)" is a method for representing biological sequences using vectors preserving inter-sequence comparability.

Last updated 26 days ago

4.70 score 3 scripts 164 downloads

MetNet - Inferring metabolic networks from untargeted high-resolution mass spectrometry data

MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information.

Last updated 2 months ago

immunooncologymetabolomicsmassspectrometrynetworkregression

4.70 score 1 scripts 177 downloads

ChIPseqR - Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

Last updated 2 months ago

chipseqinfrastructure

4.70 score 1 scripts 295 downloads

HuBMAPR - Interface to 'HuBMAP'

'HuBMAP' provides an open, global bio-molecular atlas of the human body at the cellular level. The `datasets()`, `samples()`, `donors()`, `publications()`, and `collections()` functions retrieves the information for each of these entity types. `*_details()` are available for individual entries of each entity type. `*_derived()` are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using `bulk_data_transfer()`.

Last updated 2 months ago

softwaresinglecelldataimportthirdpartyclientspatialinfrastructurebioconductor-packageclienthubmaprstudio

4.69 score 3 stars 1 scripts

RCyjs - Display and manipulate graphs in cytoscape.js

Interactive viewing and exploration of graphs, connecting R to Cytoscape.js, using websockets.

Last updated 2 months ago

visualizationgraphandnetworkthirdpartyclient

4.68 score 48 scripts 234 downloads

r3Cseq - Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.

Last updated 2 months ago

preprocessingsequencing

4.68 score 2 stars 17 scripts 394 downloads

BiGGR - Constraint based modeling in R using metabolic reconstruction databases

This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

Last updated 2 months ago

systems biologypathwaynetworkgraphandnetworkvisualizationmetabolomics

4.67 score 58 scripts 310 downloads

clipper - Gene Set Analysis Exploiting Pathway Topology

Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

Last updated 2 months ago

4.66 score 19 scripts 278 downloads

findIPs - Influential Points Detection for Feature Rankings

Feature rankings can be distorted by a single case in the context of high-dimensional data. The cases exerts abnormal influence on feature rankings are called influential points (IPs). The package aims at detecting IPs based on case deletion and quantifies their effects by measuring the rank changes (DOI:10.48550/arXiv.2303.10516). The package applies a novel rank comparing measure using the adaptive weights that stress the top-ranked important features and adjust the weights to ranking properties.

Last updated 30 days ago

geneexpressiondifferentialexpressionregressionsurvival

4.65 score 4 scripts 154 downloads

Cormotif - Correlation Motif Fit

It fits correlation motif model to multiple studies to detect study specific differential expression patterns.

Last updated 2 months ago

microarraydifferentialexpression

4.65 score 45 scripts 266 downloads

FGNet - Functional Gene Networks derived from biological enrichment analyses

Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.

Last updated 2 months ago

annotationgopathwaysgenesetenrichmentnetworkvisualizationfunctionalgenomicsnetworkenrichmentclustering

4.62 score 1 dependents 5 scripts 265 downloads

MAIT - Statistical Analysis of Metabolomic Data

The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.

Last updated 2 months ago

immunooncologymassspectrometrymetabolomicssoftware

4.60 score 20 scripts 367 downloads

RTCA - Open-source toolkit to analyse data from xCELLigence System (RTCA)

Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.

Last updated 2 months ago

immunooncologycellbasedassaysinfrastructurevisualizationtimecourse

4.60 score 4 scripts 262 downloads

limmaGUI - GUI for limma Package With Two Color Microarrays

A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.

Last updated 2 months ago

guigeneexpressiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarraytwochannelbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol

4.60 score 1 scripts 334 downloads

affylmGUI - GUI for limma Package with Affymetrix Microarrays

A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages.

Last updated 2 months ago

guigeneexpressiontranscriptiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarrayonechannelproprietaryplatformsbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol

4.60 score 3 scripts 460 downloads

crlmm - Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.

Last updated 2 months ago

microarraypreprocessingsnpcopynumbervariation

4.60 score 3 dependents 37 scripts 532 downloads

massiR - massiR: MicroArray Sample Sex Identifier

Predicts the sex of samples in gene expression microarray datasets

Last updated 2 months ago

softwaremicroarraygeneexpressionclusteringclassificationqualitycontrol

4.59 score 13 scripts 225 downloads

LPE - Methods for analyzing microarray data using Local Pooled Error (LPE) method

This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.

Last updated 2 months ago

microarraydifferentialexpression

4.58 score 1 dependents 21 scripts 298 downloads

VariantTools - Tools for Exploratory Analysis of Variant Calls

Explore, diagnose, and compare variant calls using filters.

Last updated 2 months ago

geneticsgeneticvariabilitysequencing

4.56 score 1 dependents 40 scripts 436 downloads

iBBiG - Iterative Binary Biclustering of Genesets

iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes

Last updated 2 months ago

clusteringannotationgenesetenrichment

4.56 score 2 dependents 3 scripts 240 downloads

phenoTest - Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.

Last updated 2 months ago

microarraydifferentialexpressionmultiplecomparisonclusteringclassification

4.56 score 1 dependents 9 scripts 364 downloads

flowMerge - Cluster Merging for Flow Cytometry Data

Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.

Last updated 2 months ago

immunooncologyclusteringflowcytometry

4.56 score 1 dependents 6 scripts 316 downloads

BiRewire - High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs). Since version 3.27.1 it is possible to add a constraint for dsg generation: usually positive and negative arc between two nodes could be not accepted.

Last updated 2 months ago

network

4.54 score 35 scripts 436 downloads

rsbml - R support for SBML, using libsbml

Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.

Last updated 2 months ago

graphandnetworkpathwaysnetworklibsbmlcpp

4.53 score 1 dependents 19 scripts 444 downloads

puma - Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.

Last updated 2 months ago

microarrayonechannelpreprocessingdifferentialexpressionclusteringexonarraygeneexpressionmrnamicroarraychiponchipalternativesplicingdifferentialsplicingbayesiantwochanneldataimporthta2.0

4.53 score 17 scripts 374 downloads

annotationTools - Annotate microarrays and perform cross-species gene expression analyses using flat file databases

Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).

Last updated 2 months ago

microarrayannotation

4.51 score 1 dependents 18 scripts 512 downloads

pdInfoBuilder - Platform Design Information Package Builder

Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.

Last updated 2 months ago

annotationinfrastructure

4.49 score 13 scripts 398 downloads

soGGi - Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.

Last updated 2 months ago

sequencingchipseqcoverage

4.49 score 1 dependents 51 scripts 511 downloads

vsclust - Feature-based variance-sensitive quantitative clustering

Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance. Includes several modules for statistical testing, clustering and enrichment analysis.

Last updated 1 months ago

clusteringannotationprincipalcomponentdifferentialexpressionvisualizationproteomicsmetabolomicscpp

4.48 score 9 scripts 128 downloads

rRDP - Interface to the RDP Classifier

This package installs and interfaces the naive Bayesian classifier for 16S rRNA sequences developed by the Ribosomal Database Project (RDP). With this package the classifier trained with the standard training set can be used or a custom classifier can be trained.

Last updated 2 months ago

geneticssequencinginfrastructureclassificationmicrobiomeimmunooncologyalignmentsequencematchingdataimportbayesianbioconductorbioinformaticsopenjdk

4.48 score 1 stars 3 scripts 210 downloads

MGFM - Marker Gene Finder in Microarray gene expression data

The package is designed to detect marker genes from Microarray gene expression data sets

Last updated 2 months ago

geneticsgeneexpressionmicroarray

4.48 score 1 dependents 1 scripts 217 downloads

SpacePAC - Identification of Mutational Clusters in 3D Protein Space via Simulation.

Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein's tertiary structure.

Last updated 2 months ago

clusteringproteomics

4.48 score 1 dependents 2 scripts 224 downloads

intansv - Integrative analysis of structural variations

This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.

Last updated 2 months ago

geneticsannotationsequencingsoftware

4.48 score 2 scripts 246 downloads

RSVSim - RSVSim: an R/Bioconductor package for the simulation of structural variations

RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

Last updated 2 months ago

sequencing

4.48 score 7 scripts 249 downloads

GraphPAC - Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.

Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model.

Last updated 2 months ago

clusteringproteomics

4.48 score 1 dependents 1 scripts 234 downloads

BCRANK - Predicting binding site consensus from ranked DNA sequences

Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search

Last updated 2 months ago

motifdiscoverygeneregulation

4.48 score 25 scripts 404 downloads

RBM - RBM: a R package for microarray and RNA-Seq data analysis

Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets.

Last updated 2 months ago

microarraydifferentialexpression

4.41 score 13 scripts 198 downloads

smartid - Scoring and Marker Selection Method Based on Modified TF-IDF

This package enables automated selection of group specific signature, especially for rare population. The package is developed for generating specifc lists of signature genes based on Term Frequency-Inverse Document Frequency (TF-IDF) modified methods. It can also be used as a new gene-set scoring method or data transformation method. Multiple visualization functions are implemented in this package.

Last updated 1 months ago

softwaregeneexpressiontranscriptomics

4.40 score 1 stars 2 scripts 174 downloads

immunoClust - immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

immunoClust is a model based clustering approach for Flow Cytometry samples. The cell-events of single Flow Cytometry samples are modelled by a mixture of multinominal normal- or t-distributions. The cell-event clusters of several samples are modelled by a mixture of multinominal normal-distributions aiming stable co-clusters across these samples.

Last updated 27 days ago

clusteringflowcytometrysinglecellcellbasedassaysimmunooncologygslcpp

4.38 score 4 scripts 214 downloads

COSNet - Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

Package that implements the COSNet classification algorithm. The algorithm predicts node labels in partially labeled graphs where few positives are available for the class being predicted.

Last updated 2 months ago

graphandnetworkclassificationnetworkneuralnetwork

4.38 score 1 stars 15 scripts 218 downloads

PhenStat - Statistical analysis of phenotypic data

Package contains methods for statistical analysis of phenotypic data.

Last updated 2 months ago

statisticalmethod

4.38 score 12 scripts 244 downloads

methylMnM - detect different methylation level (DMR)

To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.

Last updated 2 months ago

softwarednamethylationsequencing

4.38 score 1 dependents 2 scripts 208 downloads

msmsEDA - Exploratory Data Analysis of LC-MS/MS data by spectral counts

Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.

Last updated 2 months ago

immunooncologysoftwaremassspectrometryproteomics

4.38 score 2 dependents 4 scripts 553 downloads

geNetClassifier - Classify diseases and build associated gene networks using gene expression profiles

Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

Last updated 2 months ago

classificationdifferentialexpressionmicroarray

4.38 score 2 dependents 1 scripts 397 downloads

HybridMTest - Hybrid Multiple Testing

Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.

Last updated 2 months ago

geneexpressiongeneticsmicroarray

4.38 score 1 dependents 5 scripts 428 downloads

BAGS - A Bayesian Approach for Geneset Selection

R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.

Last updated 2 months ago

bayesian

4.38 score 40 scripts 366 downloads

anota - ANalysis Of Translational Activity (ANOTA).

Genome wide studies of translational control is emerging as a tool to study verious biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis.

Last updated 2 months ago

geneexpressiondifferentialexpressionmicroarraysequencing

4.38 score 1 dependents 2 scripts 359 downloads

a4Core - Automated Affymetrix Array Analysis Core Package

Utility functions for the Automated Affymetrix Array Analysis set of packages.

Last updated 2 months ago

microarrayclassification

4.38 score 4 dependents 2 scripts 453 downloads

snm - Supervised Normalization of Microarrays

SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

Last updated 2 months ago

microarrayonechanneltwochannelmultichanneldifferentialexpressionexonarraygeneexpressiontranscriptionmultiplecomparisonpreprocessingqualitycontrol

4.38 score 60 scripts 316 downloads

ddCt - The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

Last updated 2 months ago

geneexpressiondifferentialexpressionmicrotitreplateassayqpcr

4.38 score 8 scripts 296 downloads

plgem - Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)

The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

Last updated 2 months ago

immunooncologymicroarraydifferentialexpressionproteomicsgeneexpressionmassspectrometry

4.38 score 1 dependents 8 scripts 420 downloads

PAA - PAA (Protein Array Analyzer)

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

Last updated 2 months ago

classificationmicroarrayonechannelproteomicscpp

4.34 score 11 scripts 250 downloads

MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection

The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.

Last updated 2 months ago

sequencinggeneexpressiontranscription

4.34 score 11 scripts 224 downloads

PECA - Probe-level Expression Change Averaging

Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.

Last updated 2 months ago

softwareproteomicsmicroarraydifferentialexpressiongeneexpressionexonarraydifferentialsplicing

4.34 score 11 scripts 250 downloads

SeqGSEA - Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.

Last updated 2 months ago

sequencingrnaseqgenesetenrichmentgeneexpressiondifferentialexpressiondifferentialsplicingimmunooncology

4.34 score 11 scripts 458 downloads

DEGraph - Two-sample tests on a graph

DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.

Last updated 2 months ago

microarraydifferentialexpressiongraphandnetworknetworknetworkenrichmentdecisiontree

4.34 score 11 scripts 210 downloads

MAGAR - MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

Last updated 1 months ago

regressionepigeneticsdnamethylationsnpgeneticvariabilitymethylationarraymicroarraycpgislandmethylseqsequencingmrnamicroarraypreprocessingcopynumbervariationtwochannelimmunooncologydifferentialmethylationbatcheffectqualitycontroldataimportnetworkclusteringgraphandnetwork

4.30 score 3 scripts 274 downloads

TIN - Transcriptome instability analysis

The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.

Last updated 2 months ago

exonarraymicroarraygeneexpressionalternativesplicinggeneticsdifferentialsplicing

4.30 score 1 scripts 228 downloads

SELEX - Functions for analyzing SELEX-seq data

Tools for quantifying DNA binding specificities based on SELEX-seq data.

Last updated 2 months ago

softwaremotifdiscoverymotifannotationgeneregulationtranscriptionopenjdk

4.30 score 8 scripts 222 downloads

nethet - A bioconductor package for high-dimensional exploration of biological network heterogeneity

Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. In particular, we provide code for formal two-sample testing in Gaussian graphical models (differential network and GGM-GSA; Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (mixed graphical lasso, Stadler and Mukherjee, 2013).

Last updated 2 months ago

clusteringgraphandnetwork

4.30 score 7 scripts 240 downloads

compEpiTools - Tools for computational epigenomics

Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.

Last updated 2 months ago

geneexpressionsequencingvisualizationgenomeannotationcoverage

4.30 score 6 scripts 231 downloads

SemDist - Information Accretion-based Function Predictor Evaluation

This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.

Last updated 2 months ago

classificationannotationgosoftware

4.30 score 1 stars 3 scripts 234 downloads

CAFE - Chromosmal Aberrations Finder in Expression data

Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input

Last updated 2 months ago

geneexpressionmicroarrayonechannelgenesetenrichment

4.30 score 2 scripts 252 downloads

Clomial - Infers clonal composition of a tumor

Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

Last updated 2 months ago

geneticsgeneticvariabilitysequencingclusteringmultiplecomparisonbayesiandnaseqexomeseqtargetedresequencingimmunooncology

4.30 score 3 scripts 188 downloads

BEAT - BEAT - BS-Seq Epimutation Analysis Toolkit

Model-based analysis of single-cell methylation data

Last updated 2 months ago

immunooncologygeneticsmethylseqsoftwarednamethylationepigenetics

4.30 score 3 scripts 218 downloads

h5vc - Managing alignment tallies using a hdf5 backend

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

Last updated 2 months ago

curlbzip2xz-utilszlibcpp

4.30 score 2 scripts

dagLogo - dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Visualize significant conserved amino acid sequence pattern in groups based on probability theory.

Last updated 2 months ago

sequencematchingvisualization

4.30 score 9 scripts 268 downloads

DriverNet - Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.

Last updated 2 months ago

network

4.30 score 7 scripts 190 downloads

OSAT - OSAT: Optimal Sample Assignment Tool

A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 .

Last updated 2 months ago

datarepresentationvisualizationexperimentaldesignqualitycontrol

4.30 score 3 scripts 260 downloads

DART - Denoising Algorithm based on Relevance network Topology

Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.

Last updated 2 months ago

geneexpressiondifferentialexpressiongraphandnetworkpathways

4.30 score 1 scripts 278 downloads

CNAnorm - A normalization method for Copy Number Aberration in cancer samples

Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.

Last updated 2 months ago

copynumbervariationsequencingcoveragenormalizationwholegenomednaseqgenomicvariationfortran

4.30 score 6 scripts 260 downloads

PREDA - Position Related Data Analysis

Package for the position related analysis of quantitative functional genomics data.

Last updated 2 months ago

softwarecopynumbervariationgeneexpressiongenetics

4.30 score 9 scripts 285 downloads

TEQC - Quality control for target capture experiments

Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Last updated 2 months ago

qualitycontrolmicroarraysequencinggenetics

4.30 score 8 scripts 282 downloads

CSAR - Statistical tools for the analysis of ChIP-seq data

Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.

Last updated 2 months ago

chipseqtranscriptiongenetics

4.30 score 6 scripts 300 downloads

rbsurv - Robust likelihood-based survival modeling with microarray data

This package selects genes associated with survival.

Last updated 2 months ago

microarray

4.30 score 6 scripts 297 downloads

ACME - Algorithms for Calculating Microarray Enrichment (ACME)

ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

Last updated 2 months ago

technologymicroarraynormalization

4.30 score 4 scripts 417 downloads

SLqPCR - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH

Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH

Last updated 2 months ago

microtitreplateassayqpcr

4.30 score 2 scripts 262 downloads

cghMCR - Find chromosome regions showing common gains/losses

This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.

Last updated 2 months ago

microarraycopynumbervariation

4.30 score 1 scripts 348 downloads

genArise - Microarray Analysis tool

genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

Last updated 2 months ago

microarraytwochannelpreprocessing

4.30 score 1 scripts 237 downloads

HEM - Heterogeneous error model for identification of differentially expressed genes under multiple conditions

This package fits heterogeneous error models for analysis of microarray data

Last updated 2 months ago

microarraydifferentialexpression

4.30 score 6 scripts 309 downloads

switchBox - Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).

Last updated 2 months ago

softwarestatisticalmethodclassification

4.30 score 1 dependents 11 scripts 254 downloads

mogsa - Multiple omics data integrative clustering and gene set analysis

This package provide a method for doing gene set analysis based on multiple omics data.

Last updated 2 months ago

geneexpressionprincipalcomponentstatisticalmethodclusteringsoftware

4.29 score 49 scripts 441 downloads

SIMAT - GC-SIM-MS data processing and alaysis tool

This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.

Last updated 2 months ago

immunooncologysoftwaremetabolomicsmassspectrometry

4.26 score 1 scripts 212 downloads

ccrepe - ccrepe_and_nc.score

The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.

Last updated 2 months ago

immunooncologystatisticsmetagenomicsbioinformaticssoftware

4.26 score 7 scripts 288 downloads

a4Preproc - Automated Affymetrix Array Analysis Preprocessing Package

Utility functions to pre-process data for the Automated Affymetrix Array Analysis set of packages.

Last updated 2 months ago

microarraypreprocessing

4.26 score 3 dependents 4 scripts 465 downloads

NCIgraph - Pathways from the NCI Pathways Database

Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.

Last updated 2 months ago

pathwaysgraphandnetwork

4.26 score 1 dependents 10 scripts 218 downloads

EMDomics - Earth Mover's Distance for Differential Analysis of Genomics Data

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.

Last updated 2 months ago

softwaredifferentialexpressiongeneexpressionmicroarray

4.23 score 17 scripts 224 downloads

ASEB - Predict Acetylated Lysine Sites

ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT-family.

Last updated 2 months ago

proteomicscpp

4.20 score 1 scripts 340 downloads

GRENITS - Gene Regulatory Network Inference Using Time Series

The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.

Last updated 2 months ago

networkinferencegeneregulationtimecoursegraphandnetworkgeneexpressionnetworkbayesianopenblascpp

4.20 score 2 scripts 195 downloads

XDE - XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Multi-level model for cross-study detection of differential gene expression.

Last updated 2 months ago

microarraydifferentialexpressioncpp

4.20 score 10 scripts 316 downloads

Harshlight - A "corrective make-up" program for microarray chips

The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.

Last updated 2 months ago

microarrayqualitycontrolpreprocessingonechannelreportwriting

4.20 score 2 scripts 364 downloads

ABarray - Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.

Last updated 2 months ago

microarrayonechannelpreprocessing

4.20 score 3 scripts 447 downloads

codelink - Manipulation of Codelink microarray data

This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.

Last updated 2 months ago

microarrayonechanneldataimportpreprocessing

4.20 score 5 scripts 373 downloads

trio - Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

Last updated 2 months ago

snpgeneticvariabilitymicroarraygenetics

4.18 score 19 scripts 281 downloads

hiReadsProcessor - Functions to process LM-PCR reads from 454/Illumina data

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

Last updated 2 months ago

sequencingpreprocessing

4.18 score 7 scripts 222 downloads

erccdashboard - Assess Differential Gene Expression Experiments with ERCC Controls

Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.

Last updated 2 months ago

immunooncologygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggeneticsmicroarraymrnamicroarrayrnaseqbatcheffectmultiplecomparisonqualitycontrol

4.18 score 4 scripts 231 downloads

unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

Last updated 2 months ago

differentialexpressiongeneexpressionmicrotitreplateassaymultiplecomparisonqualitycontrolsoftwarevisualizationqpcr

4.18 score 150 downloads

LBE - Estimation of the false discovery rate

LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.

Last updated 2 months ago

multiplecomparison

4.18 score 1 scripts 454 downloads

ssize - Estimate Microarray Sample Size

Functions for computing and displaying sample size information for gene expression arrays.

Last updated 2 months ago

microarraydifferentialexpression

4.18 score 15 scripts 318 downloads

pmm - Parallel Mixed Model

The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.

Last updated 2 months ago

systemsbiologyregression

4.15 score 3 scripts 175 downloads

STATegRa - Classes and methods for multi-omics data integration

Classes and tools for multi-omics data integration.

Last updated 2 months ago

softwarestatisticalmethodclusteringdimensionreductionprincipalcomponent

4.15 score 3 scripts 220 downloads

CGHnormaliter - Normalization of array CGH data with imbalanced aberrations.

Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).

Last updated 2 months ago

microarraypreprocessing

4.15 score 1 scripts 278 downloads

plier - Implements the Affymetrix PLIER algorithm

The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.

Last updated 2 months ago

softwarecpp

4.14 score 115 scripts 354 downloads

RUVnormalize - RUV for normalization of expression array data

RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.

Last updated 2 months ago

statisticalmethodnormalization

4.11 score 32 scripts 244 downloads

DMRcaller - Differentially Methylated Regions caller

Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.

Last updated 2 months ago

differentialmethylationdnamethylationsoftwaresequencingcoverage

4.08 score 8 scripts 260 downloads

CFAssay - Statistical analysis for the Colony Formation Assay

The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.

Last updated 2 months ago

cellbasedassayscellbiologyimmunooncologyregressionsurvival

4.08 score 2 scripts 192 downloads

cleanUpdTSeq - cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.

Last updated 2 months ago

sequencing3 end sequencingpolyadenylation siteinternal priming

4.08 score 1 dependents 9 scripts 260 downloads

AffyRNADegradation - Analyze and correct probe positional bias in microarray data due to RNA degradation

The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Last updated 2 months ago

geneexpressionmicroarrayonechannelpreprocessingqualitycontrol

4.08 score 2 scripts 382 downloads

GSEAlm - Linear Model Toolset for Gene Set Enrichment Analysis

Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.

Last updated 2 months ago

microarray

4.08 score 8 scripts 324 downloads

gaga - GaGa hierarchical model for high-throughput data analysis

Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).

Last updated 2 months ago

immunooncologyonechannelmassspectrometrymultiplecomparisondifferentialexpressionclassification

4.08 score 1 dependents 9 scripts 296 downloads

OCplus - Operating characteristics plus sample size and local fdr for microarray experiments

This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).

Last updated 2 months ago

microarraydifferentialexpressionmultiplecomparison

4.08 score 2 scripts 316 downloads

IdeoViz - Plots data (continuous/discrete) along chromosomal ideogram

Plots data associated with arbitrary genomic intervals along chromosomal ideogram.

Last updated 2 months ago

visualizationmicroarray

4.05 score 25 scripts 323 downloads

gpls - Classification using generalized partial least squares

Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.

Last updated 2 months ago

classificationmicroarrayregression

4.04 score 11 scripts 484 downloads

sincell - R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.

Last updated 2 months ago

immunooncologysequencingrnaseqclusteringgraphandnetworkvisualizationgeneexpressiongenesetenrichmentbiomedicalinformaticscellbiologyfunctionalgenomicssystemsbiology

4.00 score 6 scripts 221 downloads

seq2pathway - a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.

Last updated 2 months ago

software

4.00 score 3 scripts 408 downloads

Rnits - R Normalization and Inference of Time Series data

R/Bioconductor package for normalization, curve registration and inference in time course gene expression data.

Last updated 2 months ago

geneexpressionmicroarraytimecoursedifferentialexpressionnormalization

4.00 score 1 scripts 234 downloads

UNDO - Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.

Last updated 2 months ago

software

4.00 score 6 scripts 218 downloads

TargetScore - TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information

Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

Last updated 2 months ago

mirna

4.00 score 9 scripts 248 downloads

flowBeads - flowBeads: Analysis of flow bead data

This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.

Last updated 2 months ago

immunooncologyinfrastructureflowcytometrycellbasedassays

4.00 score 7 scripts 252 downloads

EBcoexpress - EBcoexpress for Differential Co-Expression Analysis

An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level

Last updated 2 months ago

bayesian

4.00 score 6 scripts 272 downloads

PING - Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

Last updated 2 months ago

clusteringstatisticalmethodvisualizationsequencinggsl

4.00 score 7 scripts 259 downloads

ChIPsim - Simulation of ChIP-seq experiments

A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

Last updated 2 months ago

infrastructurechipseq

4.00 score 3 scripts 292 downloads

CGHbase - CGHbase: Base functions and classes for arrayCGH data analysis.

Contains functions and classes that are needed by arrayCGH packages.

Last updated 2 months ago

infrastructuremicroarraycopynumbervariation

3.98 score 8 dependents 3 scripts 742 downloads

BubbleTree - BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

CNV analysis in groups of tumor samples.

Last updated 2 months ago

copynumbervariationsoftwaresequencingcoverage

3.95 score 15 scripts 222 downloads

DynDoc - Dynamic document tools

A set of functions to create and interact with dynamic documents and vignettes.

Last updated 2 months ago

reportwritinginfrastructure

3.93 score 7 dependents 8 scripts 2.0k downloads

flowMatch - Matching and meta-clustering in flow cytometry

Matching cell populations and building meta-clusters and templates from a collection of FC samples.

Last updated 2 months ago

immunooncologyclusteringflowcytometrycpp

3.90 score 1 scripts 222 downloads

BADER - Bayesian Analysis of Differential Expression in RNA Sequencing Data

For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.

Last updated 2 months ago

immunooncologysequencingrnaseqdifferentialexpressionsoftwaresagecpp

3.90 score 1 scripts 316 downloads

antiProfiles - Implementation of gene expression anti-profiles

Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.

Last updated 2 months ago

geneexpressionclassification

3.90 score 346 downloads

iASeq - iASeq: integrating multiple sequencing datasets for detecting allele-specific events

It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies.

Last updated 2 months ago

immunooncologysnprnaseqchipseq

3.90 score 1 scripts 205 downloads

frmaTools - Frozen RMA Tools

Tools for advanced use of the frma package.

Last updated 2 months ago

softwaremicroarraypreprocessing

3.90 score 6 scripts 286 downloads

mBPCR - Bayesian Piecewise Constant Regression for DNA copy number estimation

It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.

Last updated 2 months ago

acghsnpmicroarraycopynumbervariation

3.90 score 1 scripts 284 downloads

BUS - Gene network reconstruction

This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).

Last updated 2 months ago

preprocessingcpp

3.90 score 6 scripts 252 downloads

GraphAlignment - GraphAlignment

Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006))

Last updated 2 months ago

graphandnetworknetwork

3.90 score 9 scripts 227 downloads

RLMM - A Genotype Calling Algorithm for Affymetrix SNP Arrays

A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

Last updated 2 months ago

microarrayonechannelsnpgeneticvariability

3.90 score 1 scripts 248 downloads

timecourse - Statistical Analysis for Developmental Microarray Time Course Data

Functions for data analysis and graphical displays for developmental microarray time course data.

Last updated 2 months ago

microarraytimecoursedifferentialexpression

3.90 score 7 scripts 354 downloads

clusterStab - Compute cluster stability scores for microarray data

This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.

Last updated 2 months ago

clustering

3.90 score 2 scripts 336 downloads

webbioc - Bioconductor Web Interface

An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.)

Last updated 2 months ago

infrastructuremicroarrayonechanneldifferentialexpression

3.90 score 4 scripts 424 downloads

SpeCond - Condition specific detection from expression data

This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.

Last updated 2 months ago

microarraydifferentialexpressionmultiplecomparisonclusteringreportwriting

3.89 score 13 scripts 259 downloads

tracktables - Build IGV tracks and HTML reports

Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.

Last updated 2 months ago

sequencingreportwriting

3.87 score 37 scripts 287 downloads

rain - Rhythmicity Analysis Incorporating Non-parametric Methods

This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.

Last updated 2 months ago

timecoursegeneticssystemsbiologyproteomicsmicroarraymultiplecomparison

3.86 score 18 scripts 280 downloads

MiRaGE - MiRNA Ranking by Gene Expression

The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.

Last updated 2 months ago

immunooncologymicroarraygeneexpressionrnaseqsequencingsage

3.85 score 35 scripts 244 downloads

Icens - NPMLE for Censored and Truncated Data

Many functions for computing the NPMLE for censored and truncated data.

Last updated 2 months ago

infrastructure

3.83 score 7 dependents 16 scripts 901 downloads

weaver - Tools and extensions for processing Sweave documents

This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.

Last updated 2 months ago

infrastructure

3.82 score 33 scripts 288 downloads

GeneticsPed - Pedigree and genetic relationship functions

Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care!

Last updated 2 months ago

geneticsfortrancpp

3.82 score 11 scripts 261 downloads

pandaR - PANDA Algorithm

Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.

Last updated 2 months ago

statisticalmethodgraphandnetworkmicroarraygeneregulationnetworkinferencegeneexpressiontranscriptionnetwork

3.78 score 1 dependents 8 scripts 260 downloads

flowCHIC - Analyze flow cytometric data using histogram information

A package to analyze flow cytometric data of complex microbial communities based on histogram images

Last updated 2 months ago

immunooncologycellbasedassaysclusteringflowcytometrysoftwarevisualization

3.78 score 1 scripts 211 downloads

MPFE - Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data

Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.

Last updated 2 months ago

highthroughputsequencingdatadnamethylationmethylseq

3.78 score 1 scripts 169 downloads

CNORdt - Add-on to CellNOptR: Discretized time treatments

This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.

Last updated 2 months ago

immunooncologycellbasedassayscellbiologyproteomicstimecourse

3.78 score 15 scripts 212 downloads

agilp - Agilent expression array processing package

More about what it does (maybe more than one line)

Last updated 2 months ago

3.78 score 3 scripts 406 downloads

lmdme - Linear Model decomposition for Designed Multivariate Experiments

linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.

Last updated 2 months ago

microarrayonechanneltwochannelvisualizationdifferentialexpressionexperimentdatacancer

3.78 score 1 scripts 234 downloads

ChIPXpress - ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

Last updated 2 months ago

chipchipchipseq

3.78 score 2 scripts 230 downloads

rqubic - Qualitative biclustering algorithm for expression data analysis in R

This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.

Last updated 2 months ago

clustering

3.78 score 1 dependents 4 scripts 284 downloads

a4Reporting - Automated Affymetrix Array Analysis Reporting Package

Utility functions to facilitate the reporting of the Automated Affymetrix Array Analysis Reporting set of packages.

Last updated 2 months ago

microarray

3.78 score 1 dependents 3 scripts 355 downloads

a4Classif - Automated Affymetrix Array Analysis Classification Package

Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages.

Last updated 2 months ago

microarraygeneexpressionclassification

3.78 score 1 dependents 1 scripts 410 downloads

clst - Classification by local similarity threshold

Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.

Last updated 2 months ago

classification

3.78 score 1 dependents 10 scripts 242 downloads

LiquidAssociation - LiquidAssociation

The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.

Last updated 2 months ago

pathwaysgeneexpressioncellbiologygeneticsnetworktimecourse

3.78 score 1 dependents 3 scripts 270 downloads

GeneRegionScan - GeneRegionScan

A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

Last updated 2 months ago

microarraydataimportsnponechannelvisualization

3.78 score 1 scripts 295 downloads

GeneSelectMMD - Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions

Gene selection based on a mixture of marginal distributions.

Last updated 2 months ago

differentialexpressionfortran

3.78 score 1 dependents 1 scripts 286 downloads

DFP - Gene Selection

This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.

Last updated 2 months ago

microarraydifferentialexpression

3.78 score 5 scripts 284 downloads

iterativeBMA - The Iterative Bayesian Model Averaging (BMA) algorithm

The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).

Last updated 2 months ago

microarrayclassification

3.78 score 1 scripts 262 downloads

mdqc - Mahalanobis Distance Quality Control for microarrays

MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

Last updated 2 months ago

microarrayqualitycontrol

3.78 score 1 dependents 4 scripts 414 downloads

panp - Presence-Absence Calls from Negative Strand Matching Probesets

A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

Last updated 2 months ago

infrastructure

3.78 score 2 scripts 342 downloads

diffGeneAnalysis - Performs differential gene expression Analysis

Analyze microarray data

Last updated 2 months ago

microarraydifferentialexpression

3.78 score 1 scripts 240 downloads

MVCClass - Model-View-Controller (MVC) Classes

Creates classes used in model-view-controller (MVC) design

Last updated 2 months ago

visualizationinfrastructuregraphandnetwork

3.78 score 1 dependents 376 downloads

cycle - Significance of periodic expression pattern in time-series data

Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models

Last updated 2 months ago

microarraytimecourse

3.72 score 13 scripts 298 downloads

MineICA - Analysis of an ICA decomposition obtained on genomics data

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

Last updated 2 months ago

visualizationmultiplecomparison

3.66 score 23 scripts 268 downloads

a4 - Automated Affymetrix Array Analysis Umbrella Package

Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.

Last updated 2 months ago

microarray

3.65 score 15 scripts 439 downloads

clstutils - Tools for performing taxonomic assignment

Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.

Last updated 2 months ago

sequencingclassificationvisualizationqualitycontrol

3.64 score 11 scripts 248 downloads

OpenStats - A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

Package contains several methods for statistical analysis of genotype to phenotype association in high-throughput screening pipelines.

Last updated 23 days ago

statisticalmethodbatcheffectbayesian

3.60 score 4 scripts 117 downloads

girafe - Genome Intervals and Read Alignments for Functional Exploration

The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.

Last updated 27 days ago

sequencing

3.60 score 1 scripts 296 downloads

RUVcorr - Removal of unwanted variation for gene-gene correlations and related analysis

RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.

Last updated 2 months ago

geneexpressionnormalization

3.60 score 8 scripts 217 downloads

pepXMLTab - Parsing pepXML files and filter based on peptide FDR.

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

Last updated 2 months ago

immunooncologyproteomicsmassspectrometry

3.60 score 9 scripts 223 downloads

metabomxtr - A package to run mixture models for truncated metabolomics data with normal or lognormal distributions

The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.

Last updated 2 months ago

immunooncologymetabolomicsmassspectrometry

3.60 score 5 scripts 242 downloads

INPower - An R package for computing the number of susceptibility SNPs

An R package for computing the number of susceptibility SNPs and power of future studies

Last updated 2 months ago

snp

3.60 score 1 scripts 237 downloads

rfPred - Assign rfPred functional prediction scores to a missense variants list

Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go).

Last updated 2 months ago

softwareannotationclassification

3.60 score 4 scripts 222 downloads

NetSAM - Network Seriation And Modularization

The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules.

Last updated 2 months ago

3.60 score 1 scripts 249 downloads

CNORfeeder - Integration of CellNOptR to add missing links

This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.

Last updated 2 months ago

cellbasedassayscellbiologyproteomicsnetworkinference

3.60 score 9 scripts 258 downloads

lpNet - Linear Programming Model for Network Inference

lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.

Last updated 2 months ago

networkinference

3.60 score 232 downloads

CNORfuzzy - Addon to CellNOptR: Fuzzy Logic

This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).

Last updated 2 months ago

network

3.60 score 7 scripts 242 downloads

MinimumDistance - A Package for De Novo CNV Detection in Case-Parent Trios

Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

Last updated 2 months ago

microarraysnpcopynumbervariation

3.60 score 10 scripts 319 downloads

VegaMC - VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

Last updated 2 months ago

acghcopynumbervariation

3.60 score 1 scripts 238 downloads

ternarynet - Ternary Network Estimation

Gene-regulatory network (GRN) modeling seeks to infer dependencies between genes and thereby provide insight into the regulatory relationships that exist within a cell. This package provides a computational Bayesian approach to GRN estimation from perturbation experiments using a ternary network model, in which gene expression is discretized into one of 3 states: up, unchanged, or down). The ternarynet package includes a parallel implementation of the replica exchange Monte Carlo algorithm for fitting network models, using MPI.

Last updated 2 months ago

softwarecellbiologygraphandnetworknetworkbayesiancpp

3.60 score 3 scripts 209 downloads

qpcrNorm - Data-driven normalization strategies for high-throughput qPCR data.

The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.

Last updated 2 months ago

preprocessinggeneexpression

3.60 score 3 scripts 284 downloads

biocGraph - Graph examples and use cases in Bioinformatics

This package provides examples and code that make use of the different graph related packages produced by Bioconductor.

Last updated 2 months ago

visualizationgraphandnetwork

3.60 score 576 downloads

logicFS - Identification of SNP Interactions

Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.

Last updated 2 months ago

snpclassificationgenetics

3.60 score 8 scripts 336 downloads

sizepower - Sample Size and Power Calculation in Micorarray Studies

This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice.

Last updated 2 months ago

microarray

3.60 score 3 scripts 259 downloads

copa - Functions to perform cancer outlier profile analysis.

COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.

Last updated 2 months ago

onechanneltwochanneldifferentialexpressionvisualization

3.60 score 2 scripts 302 downloads

pathRender - Render molecular pathways

build graphs from pathway databases, render them by Rgraphviz.

Last updated 2 months ago

graphandnetworkpathwaysvisualization

3.60 score 2 scripts 336 downloads

MiPP - Misclassification Penalized Posterior Classification

This package finds optimal sets of genes that seperate samples into two or more classes.

Last updated 2 months ago

microarrayclassification

3.60 score 1 scripts 292 downloads

apComplex - Estimate protein complex membership using AP-MS protein data

Functions to estimate a bipartite graph of protein complex membership using AP-MS data.

Last updated 2 months ago

immunooncologynetworkinferencemassspectrometrygraphandnetwork

3.60 score 8 scripts 491 downloads

OLINgui - Graphical user interface for OLIN

Graphical user interface for the OLIN package

Last updated 2 months ago

microarraytwochannelqualitycontrolpreprocessingvisualization

3.60 score 1 scripts 310 downloads

MetCirc - Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.

Last updated 2 months ago

shinyappsmetabolomicsmassspectrometryvisualization

3.48 score 2 scripts 244 downloads

MethTargetedNGS - Perform Methylation Analysis on Next Generation Sequencing Data

Perform step by step methylation analysis of Next Generation Sequencing data.

Last updated 2 months ago

researchfieldgeneticssequencingalignmentsequencematchingdataimport

3.48 score 1 scripts 198 downloads

QuartPAC - Identification of mutational clusters in protein quaternary structures

Identifies clustering of somatic mutations in proteins over the entire quaternary structure.

Last updated 2 months ago

clusteringproteomicssomaticmutation

3.48 score 2 scripts 201 downloads

proBAMr - Generating SAM file for PSMs in shotgun proteomics data

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

Last updated 2 months ago

immunooncologyproteomicsmassspectrometrysoftwarevisualization

3.48 score 1 scripts 211 downloads

SCAN.UPC - Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.

Last updated 2 months ago

immunooncologysoftwaremicroarraypreprocessingrnaseqtwochannelonechannel

3.48 score 15 scripts 277 downloads

REDseq - Analysis of high-throughput sequencing data processed by restriction enzyme digestion

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

Last updated 2 months ago

sequencingsequencematchingpreprocessing

3.48 score 15 scripts 300 downloads

keggorthology - graph support for KO, KEGG Orthology

graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.

Last updated 2 months ago

pathwaysgraphandnetworkvisualizationkegg

3.48 score 8 scripts 466 downloads

mCSEA - Methylated CpGs Set Enrichment Analysis

Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.

Last updated 19 days ago

immunooncologydifferentialmethylationdnamethylationepigeneticsgeneticsgenomeannotationmethylationarraymicroarraymultiplecomparisontwochannel

3.38 score 15 scripts 232 downloads

hypergraph - A package providing hypergraph data structures

A package that implements some simple capabilities for representing and manipulating hypergraphs.

Last updated 2 months ago

graphandnetwork

3.38 score 4 dependents 2 scripts 506 downloads

AHMassBank - MassBank Annotation Resources for AnnotationHub

Supplies AnnotationHub with MassBank metabolite/compound annotations bundled in CompDb SQLite databases. CompDb SQLite databases contain general compound annotation as well as fragment spectra representing fragmentation patterns of compounds' ions. MassBank data is retrieved from https://massbank.eu/MassBank and processed using helper functions from the CompoundDb Bioconductor package into redistributable SQLite databases.

Last updated 2 months ago

massspectrometryannotationhubsoftware

3.30 score 1 stars 128 downloads

mslp - Predict synthetic lethal partners of tumour mutations

An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed.

Last updated 2 months ago

pharmacogeneticspharmacogenomics

3.30 score 1 scripts 112 downloads

mirIntegrator - Integrating microRNA expression into signaling pathways for pathway analysis

Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.

Last updated 2 months ago

networkmicroarraygraphandnetworkpathwayskegg

3.30 score 1 stars 2 scripts 219 downloads

hierGWAS - Asessing statistical significance in predictive GWA studies

Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.

Last updated 2 months ago

snplinkagedisequilibriumclustering

3.30 score 1 scripts 215 downloads

acde - Artificial Components Detection of Differentially Expressed Genes

This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article 'Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).

Last updated 2 months ago

differentialexpressiontimecourseprincipalcomponentgeneexpressionmicroarraymrnamicroarray

3.30 score 1 scripts 350 downloads

FISHalyseR - FISHalyseR a package for automated FISH quantification

FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.

Last updated 2 months ago

cellbiology

3.30 score 2 scripts 190 downloads

MatrixRider - Obtain total affinity and occupancies for binding site matrices on a given sequence

Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.

Last updated 2 months ago

generegulationgeneticsmotifannotation

3.30 score 5 scripts 212 downloads

diggit - Inference of Genetic Variants Driving Cellular Phenotypes

Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm

Last updated 2 months ago

systemsbiologynetworkenrichmentgeneexpressionfunctionalpredictiongeneregulation

3.30 score 3 scripts 219 downloads

skewr - Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of 'tick' marks located above the x-axis.

Last updated 2 months ago

dnamethylationtwochannelpreprocessingqualitycontrol

3.30 score 3 scripts 200 downloads

sigsquared - Gene signature generation for functionally validated signaling pathways

By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.

Last updated 2 months ago

3.30 score 1 scripts 230 downloads

parglms - support for parallelized estimation of GLMs/GEEs

This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.

Last updated 2 months ago

3.30 score 3 scripts 240 downloads

chromDraw - chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.

ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.

Last updated 2 months ago

softwarecpp

3.30 score 1 scripts 211 downloads

rgsepd - Gene Set Enrichment / Projection Displays

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

Last updated 2 months ago

immunooncologysoftwaredifferentialexpressiongenesetenrichmentrnaseq

3.30 score 10 scripts 196 downloads

cpvSNP - Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.

Last updated 2 months ago

geneticsstatisticalmethodpathwaysgenesetenrichmentgenomicvariation

3.30 score 3 scripts 230 downloads

MBAmethyl - Model-based analysis of DNA methylation data

This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.

Last updated 2 months ago

dnamethylationmethylationarray

3.30 score 1 scripts 162 downloads

IMPCdata - Retrieves data from IMPC database

Package contains methods for data retrieval from IMPC Database.

Last updated 2 months ago

experimentdata

3.30 score 4 scripts 194 downloads

SigCheck - Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.

Last updated 2 months ago

geneexpressionclassificationgenesetenrichment

3.30 score 1 scripts 233 downloads

ASGSCA - Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models

The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA).

Last updated 2 months ago

structuralequationmodels

3.30 score 3 scripts 310 downloads

messina - Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems

Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.

Last updated 2 months ago

geneexpressiondifferentialexpressionbiomedicalinformaticsclassificationsurvivalcpp

3.30 score 1 scripts 235 downloads

Basic4Cseq - Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Last updated 2 months ago

immunooncologyvisualizationqualitycontrolsequencingcoveragealignmentrnaseqsequencematchingdataimport

3.30 score 5 scripts 344 downloads

geneRxCluster - gRx Differential Clustering

Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.

Last updated 2 months ago

sequencingclusteringgenetics

3.30 score 1 scripts 228 downloads

flowBin - Combining multitube flow cytometry data by binning

Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.

Last updated 2 months ago

immunooncologycellbasedassaysflowcytometry

3.30 score 2 scripts 241 downloads

metaSeq - Meta-analysis of RNA-Seq count data in multiple studies

The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method

Last updated 2 months ago

rnaseqdifferentialexpressionsequencingimmunooncology

3.30 score 2 scripts 232 downloads

rTRMui - A shiny user interface for rTRM

This package provides a web interface to compute transcriptional regulatory modules with rTRM.

Last updated 2 months ago

transcriptionnetworkgeneregulationgraphandnetworkgui

3.30 score 1 stars 1 scripts 247 downloads

SigFuge - SigFuge

Algorithm for testing significance of clustering in RNA-seq data.

Last updated 2 months ago

clusteringvisualizationrnaseqimmunooncology

3.30 score 3 scripts 248 downloads

paircompviz - Multiple comparison test visualization

This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.

Last updated 2 months ago

graphandnetwork

3.30 score 3 scripts 212 downloads

vtpnet - variant-transcription factor-phenotype networks

variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828

Last updated 2 months ago

network

3.30 score 1 scripts 250 downloads

tRanslatome - Comparison between multiple levels of gene expression

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.

Last updated 2 months ago

cellbiologygeneregulationregulationgeneexpressiondifferentialexpressionmicroarrayhighthroughputsequencingqualitycontrolgomultiplecomparisonsbioinformatics

3.30 score 2 scripts 438 downloads

triplex - Search and visualize intramolecular triplex-forming sequences in DNA

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Last updated 2 months ago

sequencematchinggeneregulation

3.30 score 2 scripts 262 downloads

BaseSpaceR - R SDK for BaseSpace RESTful API

A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.

Last updated 2 months ago

infrastructuredatarepresentationconnecttoolssoftwaredataimporthighthroughputsequencingsequencinggenetics

3.30 score 9 scripts 342 downloads

epigenomix - Epigenetic and gene transcription data normalization and integration with mixture models

A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

Last updated 2 months ago

chipseqgeneexpressiondifferentialexpressionclassification

3.30 score 1 scripts 239 downloads

deltaGseg - deltaGseg

Identifying distinct subpopulations through multiscale time series analysis

Last updated 2 months ago

proteomicstimecoursevisualizationclustering

3.30 score 2 scripts 187 downloads

ARRmNormalization - Adaptive Robust Regression normalization for Illumina methylation data

Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

Last updated 2 months ago

dnamethylationtwochannelpreprocessingmicroarray

3.30 score 1 scripts 318 downloads

proteinProfiles - Protein Profiling

Significance assessment for distance measures of time-course protein profiles

Last updated 2 months ago

3.30 score 3 scripts 200 downloads

cisPath - Visualization and management of the protein-protein interaction networks.

cisPath is an R package that uses web browsers to visualize and manage protein-protein interaction networks.

Last updated 2 months ago

proteomicscpp

3.30 score 9 scripts 190 downloads

DrugVsDisease - Comparison of disease and drug profiles using Gene set Enrichment Analysis

This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.

Last updated 2 months ago

microarraygeneexpressionclustering

3.30 score 8 scripts 238 downloads

iBMQ - integrated Bayesian Modeling of eQTL data

integrated Bayesian Modeling of eQTL data

Last updated 2 months ago

microarraypreprocessinggeneexpressionsnpgslopenmp

3.30 score 1 scripts 164 downloads

SNAGEE - Signal-to-Noise applied to Gene Expression Experiments

Signal-to-Noise applied to Gene Expression Experiments. Signal-to-noise ratios can be used as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.

Last updated 2 months ago

microarrayonechanneltwochannelqualitycontrol

3.30 score 3 scripts 242 downloads

matchBox - Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.

The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.

Last updated 2 months ago

softwareannotationmicroarraymultiplecomparisonvisualization

3.30 score 1 scripts 175 downloads

hapFabia - hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.

Last updated 2 months ago

geneticsgeneticvariabilitysnpsequencingvisualizationclusteringsequencematchingsoftware

3.30 score 9 scripts 244 downloads

cancerclass - Development and validation of diagnostic tests from high-dimensional molecular data

The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.

Last updated 2 months ago

cancermicroarrayclassificationvisualization

3.30 score 10 scripts 488 downloads

cnvGSA - Gene Set Analysis of (Rare) Copy Number Variants

This package is intended to facilitate gene-set association with rare CNVs in case-control studies.

Last updated 2 months ago

multiplecomparison

3.30 score 3 scripts 255 downloads

coGPS - cancer outlier Gene Profile Sets

Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies

Last updated 2 months ago

microarraydifferentialexpression

3.30 score 1 scripts 220 downloads

GEWIST - Gene Environment Wide Interaction Search Threshold

This 'GEWIST' package provides statistical tools to efficiently optimize SNP prioritization for gene-gene and gene-environment interactions.

Last updated 2 months ago

multiplecomparisongenetics

3.30 score 3 scripts 180 downloads

trigger - Transcriptional Regulatory Inference from Genetics of Gene ExpRession

This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.

Last updated 2 months ago

geneexpressionsnpgeneticvariabilitymicroarraygenetics

3.30 score 3 scripts 260 downloads

AGDEX - Agreement of Differential Expression Analysis

A tool to evaluate agreement of differential expression for cross-species genomics

Last updated 2 months ago

microarraygeneticsgeneexpression

3.30 score 6 scripts 406 downloads

dks - The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.

The dks package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated.

Last updated 2 months ago

multiplecomparisonqualitycontrol

3.30 score 1 scripts 196 downloads

RTopper - This package is designed to perform Gene Set Analysis across multiple genomic platforms

the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms.

Last updated 2 months ago

microarray

3.30 score 6 scripts 261 downloads

PANR - Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

Last updated 2 months ago

immunooncologynetworkinferencevisualizationgraphandnetworkclusteringcellbasedassays

3.30 score 2 scripts 228 downloads

Streamer - Enabling stream processing of large files

Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is 'streamed' from disk into R via a `producer' and through a series of `consumers' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details.

Last updated 2 months ago

infrastructuredataimport

3.30 score 2 scripts 258 downloads

randPack - Randomization routines for Clinical Trials

A suite of classes and functions for randomizing patients in clinical trials.

Last updated 2 months ago

statisticalmethod

3.30 score 5 scripts 220 downloads

RCASPAR - A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.

Last updated 2 months ago

acghgeneexpressiongeneticsproteomicsvisualization

3.30 score 1 scripts 183 downloads

cn.farms - cn.FARMS - factor analysis for copy number estimation

This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.

Last updated 2 months ago

microarraycopynumbervariationcpp

3.30 score 7 scripts 307 downloads

flowPlots - flowPlots: analysis plots and data class for gated flow cytometry data

Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data.

Last updated 2 months ago

immunooncologyflowcytometrycellbasedassaysvisualizationdatarepresentation

3.30 score 1 scripts 207 downloads

ibh - Interaction Based Homogeneity for Evaluating Gene Lists

This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.

Last updated 2 months ago

qualitycontroldataimportgraphandnetworknetworkenrichment

3.30 score 1 scripts 220 downloads

mosaics - MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.

Last updated 2 months ago

chipseqsequencingtranscriptiongeneticsbioinformaticscpp

3.30 score 8 scripts 438 downloads

TurboNorm - A fast scatterplot smoother suitable for microarray normalization

A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

Last updated 2 months ago

microarrayonechanneltwochannelpreprocessingdnamethylationcpgislandmethylationarraynormalization

3.30 score 1 scripts 267 downloads

ChromHeatMap - Heat map plotting by genome coordinate

The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.

Last updated 2 months ago

visualization

3.30 score 311 downloads

AgiMicroRna - Processing and Differential Expression Analysis of Agilent microRNA chips

Processing and Analysis of Agilent microRNA data

Last updated 2 months ago

microarrayagilentchiponechannelpreprocessingdifferentialexpression

3.30 score 9 scripts 452 downloads

clippda - A package for the clinical proteomic profiling data analysis

Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.

Last updated 2 months ago

proteomicsonechannelpreprocessingdifferentialexpressionmultiplecomparison

3.30 score 2 scripts 267 downloads

MiChip - MiChip Parsing and Summarizing Functions

This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.

Last updated 2 months ago

microarraypreprocessing

3.30 score 1 scripts 251 downloads

Rmagpie - MicroArray Gene-expression-based Program In Error rate estimation

Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.

Last updated 2 months ago

microarrayclassification

3.30 score 1 scripts 310 downloads

dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias

Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21)

Last updated 2 months ago

microarraytwochannelqualitycontrolpreprocessing

3.30 score 10 scripts 305 downloads

metahdep - Hierarchical Dependence in Meta-Analysis

Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies

Last updated 2 months ago

microarraydifferentialexpression

3.30 score 2 scripts 260 downloads

xmapbridge - Export plotting files to the xmapBridge for visualisation in X:Map

xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.

Last updated 2 months ago

annotationreportwritingvisualization

3.30 score 325 downloads

microRNA - Data and functions for dealing with microRNAs

Different data resources for microRNAs and some functions for manipulating them.

Last updated 2 months ago

infrastructuregenomeannotationsequencematchingcpp

3.30 score 7 scripts 390 downloads

PLPE - Local Pooled Error Test for Differential Expression with Paired High-throughput Data

This package performs tests for paired high-throughput data.

Last updated 2 months ago

proteomicsmicroarraydifferentialexpression

3.30 score 7 scripts 266 downloads

iterativeBMAsurv - The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis

The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.

Last updated 2 months ago

microarray

3.30 score 8 scripts 226 downloads

RBioinf - RBioinf

Functions and datasets and examples to accompany the monograph R For Bioinformatics.

Last updated 2 months ago

geneexpressionmicroarraypreprocessingqualitycontrolclassificationclusteringmultiplecomparisonannotation

3.30 score 2 scripts 264 downloads

vbmp - Variational Bayesian Multinomial Probit Regression

Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.

Last updated 2 months ago

classification

3.30 score 3 scripts 290 downloads

occugene - Functions for Multinomial Occupancy Distribution

Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.

Last updated 2 months ago

annotationpathways

3.30 score 228 downloads

RbcBook1 - Support for Springer monograph on Bioconductor

tools for building book

Last updated 2 months ago

software

3.30 score 1 scripts 308 downloads

splots - Visualization of high-throughput assays in microtitre plate or slide format

This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.

Last updated 2 months ago

visualizationsequencingmicrotitreplateassay

3.30 score 377 downloads

lapmix - Laplace Mixture Model in Microarray Experiments

Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes.

Last updated 2 months ago

microarrayonechanneldifferentialexpression

3.30 score 1 scripts 265 downloads

BioMVCClass - Model-View-Controller (MVC) Classes That Use Biobase

Creates classes used in model-view-controller (MVC) design

Last updated 2 months ago

visualizationinfrastructuregraphandnetwork

3.30 score 357 downloads

spikeLI - Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool

SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).

Last updated 2 months ago

microarrayqualitycontrol

3.30 score 233 downloads

OrderedList - Similarities of Ordered Gene Lists

Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.

Last updated 2 months ago

microarraydifferentialexpressionmultiplecomparison

3.30 score 9 scripts 319 downloads

maCorrPlot - Visualize artificial correlation in microarray data

Graphically displays correlation in microarray data that is due to insufficient normalization

Last updated 2 months ago

microarraypreprocessingvisualization

3.30 score 1 scripts 238 downloads

adSplit - Annotation-Driven Clustering

This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.

Last updated 2 months ago

microarrayclusteringcpp

3.30 score 1 scripts 492 downloads

MantelCorr - Compute Mantel Cluster Correlations

Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data).

Last updated 2 months ago

clustering

3.30 score 1 scripts 218 downloads

fdrame - FDR adjustments of Microarray Experiments (FDR-AME)

This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma

Last updated 2 months ago

microarraydifferentialexpressionmultiplecomparison

3.30 score 264 downloads

geneRecommender - A gene recommender algorithm to identify genes coexpressed with a query set of genes

This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.

Last updated 2 months ago

microarrayclustering

3.30 score 1 scripts 277 downloads

idiogram - idiogram

A package for plotting genomic data by chromosomal location

Last updated 2 months ago

visualization

3.30 score 6 scripts 338 downloads

sagenhaft - Collection of functions for reading and comparing SAGE libraries

This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.

Last updated 2 months ago

sage

3.30 score 8 scripts 245 downloads

nnNorm - Spatial and intensity based normalization of cDNA microarray data based on robust neural nets

This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.

Last updated 2 months ago

microarraytwochannelpreprocessing

3.30 score 1 scripts 321 downloads

goTools - Functions for Gene Ontology database

Wraper functions for description/comparison of oligo ID list using Gene Ontology database

Last updated 2 months ago

microarraygovisualization

3.30 score 1 scripts 332 downloads

arrayQuality - Assessing array quality on spotted arrays

Functions for performing print-run and array level quality assessment.

Last updated 2 months ago

microarraytwochannelqualitycontrolvisualization

3.30 score 9 scripts 515 downloads

pickgene - Adaptive Gene Picking for Microarray Expression Data Analysis

Functions to Analyze Microarray (Gene Expression) Data.

Last updated 2 months ago

microarraydifferentialexpression

3.30 score 1 scripts 246 downloads

factDesign - Factorial designed microarray experiment analysis

This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.

Last updated 2 months ago

microarraydifferentialexpression

3.30 score 1 scripts 324 downloads

MeasurementError.cor - Measurement Error model estimate for correlation coefficient

Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation

Last updated 2 months ago

statisticalmethod

3.30 score 1 scripts 235 downloads

ScreenR - Package to Perform High Throughput Biological Screening

ScreenR is a package suitable to perform hit identification in loss of function High Throughput Biological Screenings performed using barcoded shRNA-based libraries. ScreenR combines the computing power of software such as edgeR with the simplicity of use of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts, and integrates a wide range of visualization modes for each step of the analysis.

Last updated 2 months ago

softwareassaydomaingeneexpressionhigh-throughput-screening

3.11 score 1 stars 13 scripts 118 downloads

ffpe - Quality assessment and control for FFPE microarray expression data

Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Last updated 2 months ago

microarraygeneexpressionqualitycontrol

3.03 score 27 scripts 252 downloads

annmap - Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071

Last updated 2 months ago

annotationmicroarrayonechannelreportwritingtranscriptionvisualization

3.00 score 2 scripts 354 downloads

a4Base - Automated Affymetrix Array Analysis Base Package

Base utility functions are available for the Automated Affymetrix Array Analysis set of packages.

Last updated 2 months ago

microarray

2.92 score 1 dependents 14 scripts 476 downloads

twilight - Estimation of local false discovery rate

In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.

Last updated 2 months ago

microarraydifferentialexpressionmultiplecomparison

2.92 score 1 dependents 14 scripts 370 downloads

bcSeq - Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.

Last updated 2 months ago

immunooncologyalignmentcrisprsequencingsequencematchingmultiplesequencealignmentsoftwareatacseqcpp

2.78 score 2 scripts 182 downloads

ExiMiR - R functions for the normalization of Exiqon miRNA array data

This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.

Last updated 2 months ago

microarrayonechanneltwochannelpreprocessinggeneexpressiontranscription

2.78 score 3 scripts 271 downloads

Rtreemix - Rtreemix: Mutagenetic trees mixture models.

Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.

Last updated 2 months ago

statisticalmethodcpp

2.68 score 12 scripts 296 downloads

maskBAD - Masking probes with binding affinity differences

Package includes functions to analyze and mask microarray expression data.

Last updated 2 months ago

microarray

2.60 score 262 downloads

bgx - Bayesian Gene eXpression

Bayesian integrated analysis of Affymetrix GeneChips

Last updated 2 months ago

microarraydifferentialexpressioncppglibc

2.60 score 1 scripts 466 downloads

CoCiteStats - Different test statistics based on co-citation.

A collection of software tools for dealing with co-citation data.

Last updated 2 months ago

software

2.60 score 288 downloads

roastgsa - Rotation based gene set analysis

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

Last updated 2 months ago

microarraypreprocessingnormalizationgeneexpressionsurvivaltranscriptionsequencingtranscriptomicsbayesianclusteringregressionrnaseqmicrornaarraymrnamicroarrayfunctionalgenomicssystemsbiologyimmunooncologydifferentialexpressiongenesetenrichmentbatcheffectmultiplecomparisonqualitycontroltimecoursemetabolomicsproteomicsepigeneticscheminformaticsexonarrayonechanneltwochannelproprietaryplatformscellbiologybiomedicalinformaticsalternativesplicingdifferentialsplicingdataimportpathways

2.30 score 120 downloads

CTDquerier - Package for CTDbase data query, visualization and downstream analysis

Package to retrieve and visualize data from the Comparative Toxicogenomics Database (http://ctdbase.org/). The downloaded data is formated as DataFrames for further downstream analyses.

Last updated 2 months ago

softwarebiomedicalinformaticsinfrastructuredataimportdatarepresentationgenesetenrichmentnetworkenrichmentpathwaysnetworkgokegg

2.30 score 2 scripts 167 downloads

maPredictDSC - Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge

This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.

Last updated 2 months ago

microarrayclassification

2.30 score 2 scripts 250 downloads

prebs - Probe region expression estimation for RNA-seq data for improved microarray comparability

The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.

Last updated 2 months ago

immunooncologymicroarrayrnaseqsequencinggeneexpressionpreprocessing

2.30 score 1 scripts 250 downloads

pvac - PCA-based gene filtering for Affymetrix arrays

The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

Last updated 2 months ago

microarrayonechannelqualitycontrol

2.30 score 2 scripts 274 downloads

TypeInfo - Optional Type Specification Prototype

A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions. Additionally, the arguments in a call to a typed function can be validated using the type specifications. We allow types to be specified as either i) by class name using either inheritance - is(x, className), or strict instance of - class(x) %in% className, or ii) a dynamic test given as an R expression which is evaluated at run-time. More precise information and interesting tests can be done via ii), but it is harder to use this information as meta-data as it requires more effort to interpret it and it is of course run-time information. It is typically more meaningful.

Last updated 2 months ago

infrastructure

2.30 score 5 scripts 255 downloads

stepNorm - Stepwise normalization functions for cDNA microarrays

Stepwise normalization functions for cDNA microarray data.

Last updated 2 months ago

microarraytwochannelpreprocessing

2.30 score 2 scripts 318 downloads

GraphAT - Graph Theoretic Association Tests

Functions and data used in Balasubramanian, et al. (2004)

Last updated 2 months ago

networkgraphandnetwork

2.30 score 4 scripts 304 downloads

ecolitk - Meta-data and tools for E. coli

Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.

Last updated 2 months ago

annotationvisualization

2.30 score 1 scripts 304 downloads

daMA - Efficient design and analysis of factorial two-colour microarray data

This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted)

Last updated 2 months ago

microarraytwochanneldifferentialexpression

2.30 score 354 downloads