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 days ago
bioconductor-package
12.59 score 12 dependencies 1170 dependentsTVTB - 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 1 days ago
bioconductor-package
0.82 score 163 dependenciesClustIRR - Clustering of immune receptor repertoires
ClustIRR is a quantitative method for clustering of immune receptor repertoires (IRRs). The algorithm identifies groups of T or B cell receptors (TCRs or BCRs) with possibly similar specificity directly from the sequences of their complementarity determining regions. ClustIRR uses graphs to visualize the specificity structures of IRRs.
Last updated 2 days ago
bioconductor-package
2.38 score 61 dependenciesMOSim - 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 days ago
bioconductor-package
2.50 score 189 dependenciesQFeatures - 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 days ago
bioconductor-package
4.80 score 98 dependencies 45 dependentsgDRimport - 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 2 days ago
bioconductor-package
2.38 score 197 dependencies 1 dependentsgDRutils - 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 2 days ago
bioconductor-package
2.86 score 106 dependencies 3 dependentsggkegg - KEGG pathway visualization by ggplot2
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 days ago
bioconductor-package
2.00 score 92 dependencies 1 dependentsBiocSingular - 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 days ago
bioconductor-package
6.11 score 28 dependencies 94 dependentslute - 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 days ago
bioconductor-package
1.51 score 88 dependenciesscDotPlot - 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 3 days ago
bioconductor-package
0.49 score 197 dependenciesIRanges - 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 3 days ago
bioconductor-package
13.90 score 2 dependencies 1716 dependentsS4Vectors - 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 3 days ago
bioconductor-package
13.93 score 1 dependencies 1783 dependentsscuttle - 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 3 days ago
bioconductor-package
5.74 score 42 dependencies 75 dependentsS4Arrays - 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 3 days ago
bioconductor-package
12.58 score 7 dependencies 1171 dependentsDelayedArray - 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 3 days ago
bioconductor-package
12.60 score 13 dependencies 1169 dependentsAnVIL - 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 3 days ago
bioconductor-package
3.33 score 68 dependencies 10 dependentspathlinkR - 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 4 days ago
bioconductor-package
2.05 score 177 dependencieslefser - R implementation of the LEfSE method for microbiome biomarker discovery
lefser is an implementation in R of the popular "LDA Effect Size (LEfSe)" method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.
Last updated 4 days ago
bioconductor-package
2.00 score 82 dependenciesspoon - 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 4 days ago
bioconductor-package
1.31 score 83 dependenciesfaers - 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 4 days ago
bioconductor-package
1 stars 1.58 score 70 dependenciesrawDiag - 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 5 days ago
bioconductor-package
1.80 score 70 dependenciespdInfoBuilder - 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 5 days ago
bioconductor-package
1.85 score 55 dependenciesmetabolomicsWorkbenchR - 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 5 days ago
bioconductor-package
1.00 score 61 dependenciescbaf - 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 5 days ago
bioconductor-package
1.16 score 144 dependencieshdxmsqc - 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 6 days ago
bioconductor-package
0.71 score 112 dependenciesSGCP - 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 6 days ago
bioconductor-package
0.49 score 150 dependenciesGDSArray - 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 8 days ago
bioconductor-package
1.58 score 30 dependencies 2 dependentsplotgardener - 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 8 days ago
bioconductor-package
2.31 score 93 dependencies 3 dependentsevaluomeR - 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 8 days ago
bioconductor-package
0.82 score 114 dependenciesDEGreport - 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 8 days ago
bioconductor-package
1.69 score 110 dependencies 1 dependentsSummarizedExperiment - SummarizedExperiment container
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 8 days ago
bioconductor-package
12.48 score 27 dependencies 1129 dependentsHoloFoodR - 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 9 days ago
bioconductor-package
1.00 score 75 dependencieshermes - 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 9 days ago
bioconductor-package
2.35 score 124 dependencies 1 dependentsscRNAseqApp - 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 9 days ago
bioconductor-package
1.90 score 223 dependenciesCATALYST - 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 9 days ago
bioconductor-package
1.80 score 170 dependencies 2 dependentsDMRcate - 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 9 days ago
bioconductor-package
2.05 score 210 dependencies 1 dependentsCardinal - 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 9 days ago
bioconductor-package
2.09 score 56 dependenciesAlphaMissenseR - 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 10 days ago
bioconductor-package
1.69 score 62 dependenciesvelociraptor - 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 10 days ago
bioconductor-package
1.45 score 61 dependencieshoodscanR - 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 10 days ago
bioconductor-package
1.31 score 108 dependenciessesame - 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 10 days ago
bioconductor-package
2.27 score 104 dependencies 1 dependentsBiocCheck - 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 10 days ago
bioconductor-package
3.11 score 67 dependencies 5 dependentsscBubbletree - Quantitative visual exploration of scRNA-seq data
scBubbletree is a quantitative method for visual exploration of scRNA-seq data. It preserves biologically meaningful properties of scRNA-seq data, such as local and global cell distances, as well as the density distribution of cells across the sample. scBubbletree is scalable and avoids the overplotting problem, and is able to visualize diverse cell attributes derived from multiomic single-cell experiments. Importantly, Importantly, scBubbletree is easy to use and to integrate with popular approaches for scRNA-seq data analysis.
Last updated 11 days ago
bioconductor-package
0.82 score 161 dependenciesPhyloProfile - 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 11 days ago
bioconductor-package
1.64 score 125 dependenciesGeDi - 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 11 days ago
bioconductor-package
1.90 score 191 dependenciesspillR - 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 11 days ago
bioconductor-package
1.58 score 171 dependenciescytoviewer - 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 11 days ago
bioconductor-package
1.16 score 141 dependenciesCepo - 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 11 days ago
bioconductor-package
1.08 score 97 dependencies 1 dependentsginmappeR - 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 12 days ago
bioconductor-package
1.45 score 64 dependenciespgxRpi - 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 12 days ago
bioconductor-package
1.51 score 117 dependenciesstandR - 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 12 days ago
bioconductor-package
1.31 score 141 dependenciesPigengene - 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 13 days ago
bioconductor-package
1.45 score 174 dependencies 1 dependentsalabaster.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 14 days ago
bioconductor-package
2.22 score 25 dependencies 7 dependentsalabaster.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 14 days ago
bioconductor-package
3.24 score 11 dependencies 12 dependentsalabaster.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 14 days ago
bioconductor-package
2.63 score 25 dependencies 7 dependentsResidualMatrix - 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 15 days ago
bioconductor-package
2.05 score 14 dependencies 7 dependentsscater - 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 15 days ago
bioconductor-package
4.80 score 97 dependencies 42 dependentszellkonverter - 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 15 days ago
bioconductor-package
1.95 score 43 dependencies 2 dependentsgemma.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 15 days ago
bioconductor-package
2.50 score 63 dependenciesgypsum - 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 15 days ago
bioconductor-package
1.90 score 16 dependencies 1 dependentsCardinalIO - 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 16 days ago
bioconductor-package
1.69 score 18 dependencies 1 dependentsHDF5Array - HDF5 backend for DelayedArray objects
Implement 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 16 days ago
bioconductor-package
6.68 score 17 dependencies 123 dependentswateRmelon - 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 16 days ago
bioconductor-package
2.27 score 157 dependencies 4 dependentsrDGIdb - R Wrapper for DGIdb
The rDGIdb package provides a wrapper for the Drug Gene Interaction Database (DGIdb). For simplicity, the wrapper query function and output resembles the user interface and results format provided on the DGIdb website (https://www.dgidb.org/).
Last updated 16 days ago
bioconductor-package
1.24 score 8 dependenciesORFik - 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 16 days ago
bioconductor-package
2.73 score 129 dependencies 2 dependentsSpatialExperiment - 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 16 days ago
bioconductor-package
5.06 score 64 dependencies 53 dependentsggmanh - 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 16 days ago
bioconductor-package
1.24 score 58 dependenciesEpiDISH - 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 whole blood, 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 16 days ago
bioconductor-package
1.69 score 17 dependencies 4 dependentstxdbmaker - 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 16 days ago
bioconductor-package
5.84 score 92 dependencies 83 dependentsscDblFinder - 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 17 days ago
bioconductor-package
1.80 score 121 dependencies 1 dependentslemur - 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 17 days ago
bioconductor-package
2.09 score 85 dependenciesBioTIP - BioTIP: An R package for characterization of Biological Tipping-Point
Adopting tipping-point theory to transcriptome profiles to unravel disease regulatory trajectory.
Last updated 17 days ago
bioconductor-package
1.16 score 73 dependenciesmia - 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 18 days ago
bioconductor-package
3.49 score 173 dependencies 6 dependentsTargetSearch - 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 18 days ago
bioconductor-package
2.00 score 2 dependenciesCoGAPS - 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 18 days ago
bioconductor-package
2.38 score 81 dependencies 1 dependentsbeadarray - 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 18 days ago
bioconductor-package
1.80 score 71 dependencies 4 dependentstrackViewer - 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 19 days ago
bioconductor-package
2.22 score 156 dependencies 1 dependentsKEGGREST - 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 19 days ago
bioconductor-package
11.34 score 19 dependencies 771 dependentsSANTA - 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 19 days ago
bioconductor-package
1.16 score 11 dependenciesepiregulon - 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 19 days ago
bioconductor-package
2.05 score 200 dependenciespRoloc - 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 20 days ago
bioconductor-package
2.00 score 219 dependencies 2 dependentsGSAR - Gene Set Analysis in R
Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.
Last updated 20 days ago
bioconductor-package
0.91 score 11 dependencieslimma - Linear Models for Microarray Data
Data analysis, linear models and differential expression for microarray and RNA-seq data.
Last updated 22 days ago
bioconductor-package
19.36 score 1 dependencies 586 dependentsfenr - 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 22 days ago
bioconductor-package
1.51 score 85 dependenciesmatter - Scientific computing for out-of-memory signals and images
Toolbox for out-of-memory scientific computing and data visualization, providing memory-efficient file-based data structures for dense and sparse vectors, matrices, and arrays with applications to nonuniformly sampled signals and images.
Last updated 22 days ago
bioconductor-package
2.42 score 15 dependencies 2 dependentsvariancePartition - 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 23 days ago
bioconductor-package
2.86 score 97 dependencies 3 dependentspadma - 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 23 days ago
bioconductor-package
0.61 score 130 dependenciesDOSE - 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 23 days ago
bioconductor-package
5.31 score 83 dependencies 58 dependentsENmix - 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 23 days ago
bioconductor-package
1.58 score 149 dependenciessechm - 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 24 days ago
bioconductor-package
1.00 score 72 dependencies 1 dependentsbigmelon - Illumina methylation array analysis for large experiments
Methods for working with Illumina arrays using gdsfmt.
Last updated 24 days ago
bioconductor-package
1.45 score 159 dependenciesstatTarget - 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 24 days ago
bioconductor-package
1.08 score 18 dependenciesglmGamPoi - 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 24 days ago
bioconductor-package
2.09 score 43 dependencies 4 dependentssparseMatrixStats - 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 24 days ago
bioconductor-package
7.49 score 5 dependencies 177 dependentsgoseq - 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 24 days ago
bioconductor-package
2.18 score 98 dependencies 6 dependentsnetboost - 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 24 days ago
bioconductor-package
0.91 score 111 dependencieslisaClust - 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 24 days ago
bioconductor-package
1.00 score 171 dependenciesDECIPHER - Tools for curating, analyzing, and manipulating biological sequences
A toolset for deciphering and managing biological sequences.
Last updated 25 days ago
bioconductor-package
3.33 score 19 dependencies 15 dependentsapeglm - 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 25 days ago
bioconductor-package
2.38 score 39 dependencies 8 dependentssimona - Semantic Similarity in 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 25 days ago
bioconductor-package
1.80 score 58 dependenciesPirat - 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 25 days ago
bioconductor-package
1.75 score 68 dependenciesGenomicRanges - 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 25 days ago
bioconductor-package
12.81 score 16 dependencies 1258 dependentsAPL - 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 26 days ago
bioconductor-package
1.31 score 176 dependenciesBiocStyle - 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 26 days ago
bioconductor-package
4.63 score 28 dependencies 41 dependentsgDRstyle - 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 26 days ago
bioconductor-package
2.18 score 87 dependenciesMsBackendRawFileReader - 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 26 days ago
bioconductor-package
1.24 score 22 dependenciesrawrr - Direct Access to Orbitrap Data and Beyond
This package wraps the functionality of the RawFileReader .NET 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 26 days ago
bioconductor-package
1.95 score 0 dependencies 2 dependentsAlpsNMR - 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 27 days ago
bioconductor-package
1.24 score 119 dependenciestximeta - 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 28 days ago
bioconductor-package
2.00 score 101 dependencies 1 dependentsMultiAssayExperiment - 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 28 days ago
bioconductor-package
7.04 score 49 dependencies 141 dependentssquallms - 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 28 days ago
bioconductor-package
1.00 score 177 dependenciesBiostrings - 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 29 days ago
bioconductor-package
13.00 score 17 dependencies 1338 dependentsVoyager - 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 29 days ago
bioconductor-package
1.31 score 159 dependenciesPIPETS - 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 29 days ago
bioconductor-package
1.31 score 32 dependenciesGSVA - 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 30 days ago
bioconductor-package
4.25 score 93 dependencies 26 dependentsTENxIO - 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
bioconductor-package
1.08 score 59 dependencies 1 dependentsSharedObject - 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 1 months ago
bioconductor-package
1.00 score 3 dependencies 1 dependentsSpectra - 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 1 months ago
bioconductor-package
5.94 score 20 dependencies 29 dependentsgDRcore - 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 1 months ago
bioconductor-package
2.73 score 107 dependencies 1 dependentsbroadSeq - 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 1 months ago
bioconductor-package
1 stars 1.24 score 221 dependenciesBioGA - 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 1 months ago
1.08 score 87 dependenciesepiNEM - 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 1 months ago
bioconductor-package
1.75 score 102 dependencies 3 dependentsoligo - 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 1 months ago
bioconductor-package
6.45 score 54 dependencies 11 dependentsggseqalign - 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 1 months ago
bioconductor-package
0.49 score 49 dependenciesRnBeads - RnBeads
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Last updated 1 months ago
bioconductor-package
6.32 score 156 dependencies 1 dependentsmotifTestR - 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 1 months ago
bioconductor-package
1.24 score 55 dependenciesbeachmat - 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 1 months ago
bioconductor-package
6.86 score 15 dependencies 130 dependentsiSEE - 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 1 months ago
bioconductor-package
3.64 score 112 dependencies 8 dependentsBiocSklearn - 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 1 months ago
bioconductor-package
1.00 score 41 dependenciesSTRINGdb - 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 1 months ago
bioconductor-package
6.06 score 43 dependencies 9 dependentsmiaViz - 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 1 months ago
bioconductor-package
2.05 score 145 dependenciesASICS - 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 1 months ago
bioconductor-package
0.91 score 121 dependenciesMoleculeExperiment - 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 1 months ago
bioconductor-package
1.75 score 116 dependenciesOmnipathR - 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 1 months ago
bioconductor-package
2.50 score 73 dependencies 2 dependentsgDR - 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 1 months ago
bioconductor-package
1.85 score 199 dependenciesBindingSiteFinder - 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
bioconductor-package
1.80 score 135 dependenciesCompoundDb - 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 1 months ago
bioconductor-package
1.45 score 110 dependencies 1 dependentsseqsetvis - 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 1 months ago
bioconductor-package
1.69 score 98 dependenciesimmunoClust - 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 1 months ago
bioconductor-package
1.31 score 12 dependenciescypress - 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 1 months ago
bioconductor-package
1.45 score 129 dependenciessmartid - 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
bioconductor-package
0.61 score 94 dependenciesGenomeInfoDb - 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 1 months ago
bioconductor-package
13.64 score 13 dependencies 1634 dependentsSingleR - 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 months ago
bioconductor-package
1.69 score 47 dependencies 1 dependentsbeachmat.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
bioconductor-package
0.36 score 20 dependenciesBiocPkgTools - 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 1 months ago
bioconductor-package
2.14 score 101 dependenciesSingleCellExperiment - 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 2 months ago
bioconductor-package
8.37 score 28 dependencies 255 dependentsalabaster.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 2 months ago
bioconductor-package
1.08 score 77 dependencies 1 dependentsalabaster.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
bioconductor-package
1.64 score 41 dependencies 3 dependentsalabaster.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
bioconductor-package
2.14 score 39 dependencies 6 dependentsMfuzz - Soft clustering of time series gene expression data
Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)
Last updated 2 months ago
bioconductor-package
1.58 score 9 dependencies 4 dependentssimpleSeg - 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
bioconductor-package
1.38 score 141 dependenciesDelayedMatrixStats - 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
bioconductor-package
7.32 score 16 dependencies 164 dependentsMSstatsTMT - 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 2 months ago
bioconductor-package
1.75 score 94 dependencies 3 dependentsAnnotationForge - 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
bioconductor-package
3.62 score 41 dependencies 20 dependentstidySpatialExperiment - 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
bioconductor-package
1.85 score 112 dependenciesspicyR - 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 2 months ago
bioconductor-package
2.18 score 154 dependencies 1 dependentsMMUPHin - 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
bioconductor-package
0.91 score 137 dependenciesQuasR - 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
bioconductor-package
1.75 score 108 dependencies 1 dependentsmonaLisa - 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
bioconductor-package
0.91 score 134 dependenciesinfercnv - 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
bioconductor-package
1.58 score 189 dependenciesPIUMA - 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
bioconductor-package
1.16 score 105 dependenciesSpatialFeatureExperiment - 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 months ago
bioconductor-package
2.46 score 137 dependencies 1 dependentsRdisop - Decomposition of Isotopic Patterns
Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Last updated 2 months ago
bioconductor-package
1.95 score 1 dependencies 4 dependentsMetaboAnnotation - 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 2 months ago
bioconductor-package
1.58 score 135 dependenciesGenomicDataCommons - NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Last updated 2 months ago
bioconductor-package
2.70 score 49 dependencies 10 dependentsfunOmics - 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
bioconductor-package
0.82 score 83 dependenciesshiny.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
bioconductor-package
1.16 score 36 dependencies 1 dependentsMSnbase - 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 2 months ago
bioconductor-package
4.55 score 126 dependencies 33 dependentsNanoMethViz - 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
bioconductor-package
2.31 score 139 dependenciesChIPseeker - 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
bioconductor-package
2.46 score 143 dependencies 5 dependentsBREW3R.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
bioconductor-package
0.61 score 18 dependenciesopenCyto - 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
bioconductor-package
1.69 score 69 dependencies 1 dependentstidybulk - 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
bioconductor-package
2.09 score 99 dependencies 1 dependentsHIBAG - 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 2 months ago
bioconductor-package
1.69 score 1 dependenciesedgeR - 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 2 months ago
bioconductor-package
8.65 score 5 dependencies 279 dependentsdiffHic - 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 2 months ago
bioconductor-package
1.08 score 61 dependenciestidySingleCellExperiment - 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
bioconductor-package
2.09 score 91 dependencies 2 dependentsiCARE - Individualized Coherent Absolute Risk Estimation (iCARE)
An R package to build, validate and apply absolute risk models
Last updated 2 months ago
bioconductor-package
1.00 score 67 dependenciesBanksy - 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
bioconductor-package
1.90 score 101 dependenciesRcwl - 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
bioconductor-package
1.38 score 102 dependencies 2 dependentsmobileRNA - 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
bioconductor-package
2.27 score 127 dependenciessmoothclust - 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
bioconductor-package
1.08 score 81 dependenciesxcms - 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 2 months ago
bioconductor-package
6.10 score 136 dependencies 12 dependentsTBSignatureProfiler - 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 2 months ago
bioconductor-package
1.58 score 168 dependenciesClusterFoldSimilarity - 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
bioconductor-package
1.51 score 168 dependenciesMSstatsConvert - 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 2 months ago
bioconductor-package
2.31 score 5 dependencies 7 dependentsrtracklayer - 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
bioconductor-package
10.51 score 48 dependencies 473 dependentsmotifStack - 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
bioconductor-package
3.08 score 136 dependencies 5 dependentssplatter - 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 2 months ago
bioconductor-package
2.05 score 54 dependencies 2 dependentsEnrichmentBrowser - 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
bioconductor-package
3.11 score 88 dependencies 3 dependentsmultiWGCNA - 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
bioconductor-package
1.24 score 138 dependenciesextraChIPs - 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
bioconductor-package
1.85 score 167 dependenciestidyFlowCore - 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
bioconductor-package
0.49 score 46 dependenciesisomiRs - Analyze isomiRs and miRNAs from small RNA-seq
Characterization of miRNAs and isomiRs, clustering and differential expression.
Last updated 2 months ago
bioconductor-package
1.64 score 142 dependenciesqsvaR - 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 2 months ago
bioconductor-package
1.08 score 148 dependenciesRMassBank - 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
bioconductor-package
3.00 score 164 dependenciesrhdf5client - 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
bioconductor-package
1.69 score 24 dependencies 2 dependentsMungeSumstats - 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 2 months ago
bioconductor-package
2.09 score 91 dependenciesRBioFormats - 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
bioconductor-package
1.24 score 40 dependencies 1 dependentsrBLAST - 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
bioconductor-package
1.16 score 50 dependenciesRCyjs - 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
bioconductor-package
1.00 score 13 dependenciesupdateObject - 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
bioconductor-package
0.61 score 3 dependenciesRhtslib - 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 2 months ago
bioconductor-package
10.54 score 1 dependencies 583 dependentsGenomicAlignments - 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
bioconductor-package
10.24 score 41 dependencies 522 dependentsGenomicFeatures - Conveniently import and query gene models
A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.
Last updated 2 months ago
bioconductor-package
9.04 score 67 dependencies 332 dependentsBSgenomeForge - Forge BSgenome data packages
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
bioconductor-package
1.38 score 50 dependenciesBSgenome - 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
bioconductor-package
8.50 score 49 dependencies 268 dependentsepiregulon.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
bioconductor-package
1.24 score 176 dependenciesfindIPs - 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 2 months ago
bioconductor-package
1.16 score 38 dependenciesSingleCellAlleleExperiment - 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 months ago
bioconductor-package
1.85 score 38 dependenciesgINTomics - 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
bioconductor-package
2.00 score 227 dependenciesmosdef - 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 months ago
bioconductor-package
1.85 score 176 dependenciesSpotSweeper - 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. Scales linearly with the number of spots and is designed to be used with 'SpatialExperiment' objects.
Last updated 2 months ago
bioconductor-package
1.69 score 100 dependenciesggtreeSpace - 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
bioconductor-package
0.82 score 95 dependenciesmultistateQTL - 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
bioconductor-package
1.00 score 107 dependenciesUPDhmm - 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
bioconductor-package
0.71 score 71 dependenciespwalign - 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 2 months ago
bioconductor-package
6.26 score 18 dependencies 104 dependentsbaySeq - 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
bioconductor-package
1.85 score 24 dependencies 3 dependentsSpaceMarkers - 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
bioconductor-package
1.24 score 77 dependenciesClustAll - ClustAll: Data driven strategy to find groups 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
bioconductor-package
1.38 score 179 dependenciesUCSC.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
bioconductor-package
13.62 score 10 dependencies 1634 dependentsiSEEfier - 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
bioconductor-package
1.00 score 118 dependenciesknowYourCG - Functional analysis of DNA methylome datasets
knowYourCG automates the functional analysis of DNA methylation data. The package tests the enrichment of discrete CpG probes across thousands of curated biological and technical features. GSEA-like analysis can be performed on continuous methylation data query sets. knowYourCG can also take beta matrices as input to perform feature aggregation over the curated database sets.
Last updated 2 months ago
bioconductor-package
1.75 score 72 dependenciesMGnifyR - 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
bioconductor-package
1.75 score 178 dependenciesCaMutQC - 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
bioconductor-package
1.90 score 167 dependenciesHybridExpress - 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
bioconductor-package
1.24 score 80 dependenciesGrafGen - 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 2 months ago
bioconductor-package
0.82 score 115 dependenciesmethyLImp2 - 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
bioconductor-package
1.00 score 39 dependenciesDegCre - 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 2 months ago
bioconductor-package
1.24 score 95 dependenciestreeclimbR - 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
bioconductor-package
1.24 score 156 dependenciesbettr - 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
bioconductor-package
1.16 score 126 dependenciessimPIC - 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
bioconductor-package
0.82 score 61 dependenciesMEIGOR - 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
bioconductor-package
1.64 score 69 dependenciestpSVG - 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
bioconductor-package
0.82 score 75 dependenciessketchR - 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 2 months ago
bioconductor-package
0.82 score 56 dependenciescrisprShiny - 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
bioconductor-package
1.00 score 184 dependenciesPedixplorer - 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
bioconductor-package
1.16 score 59 dependenciestidyomics - 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
bioconductor-package
1.08 score 196 dependenciestransmogR - 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
bioconductor-package
1.24 score 89 dependenciesSurfR - 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 2 months ago
bioconductor-package
1.51 score 183 dependenciesbiocroxytest - 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
bioconductor-package
0.61 score 29 dependenciesigvShiny - 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
bioconductor-package
1.75 score 74 dependenciestidyCoverage - 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
bioconductor-package
1.00 score 68 dependenciesVisiumIO - 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 2 months ago
bioconductor-package
0.71 score 80 dependenciesCRISPRball - 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 2 months ago
bioconductor-package
1.00 score 211 dependenciesbetaHMM - 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 2 months ago
bioconductor-package
1.00 score 69 dependenciesbiomvRCNS - 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
bioconductor-package
1.38 score 148 dependenciesBERT - Hierarchical Batch-Effect Adjustment with Trees
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 2 months ago
bioconductor-package
1.00 score 93 dependenciesCTexploreR - 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
bioconductor-package
1.31 score 100 dependenciesQTLExperiment - 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
bioconductor-package
1.45 score 67 dependencies 1 dependentsdecontX - 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
bioconductor-package
0.82 score 228 dependenciesregionalpcs - 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
bioconductor-package
0.91 score 80 dependenciesGNOSIS - 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
bioconductor-package
0.82 score 282 dependenciesscider - 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
bioconductor-package
1.58 score 133 dependenciesphantasusLite - 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
bioconductor-package
1.38 score 34 dependencies 1 dependentsMSstatsBig - 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
bioconductor-package
0.91 score 114 dependenciesraer - 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
bioconductor-package
1.90 score 70 dependenciesggsc - 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
bioconductor-package
1.80 score 165 dependenciesgatom - 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
bioconductor-package
1.31 score 118 dependenciesBioCartaImage - 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
bioconductor-package
0.71 score 4 dependenciesCCPlotR - 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
bioconductor-package
1.31 score 87 dependenciesBiocBook - 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
bioconductor-package
1.75 score 76 dependenciesplasmut - 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
bioconductor-package
1.64 score 16 dependenciesgg4way - 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
bioconductor-package
0.91 score 82 dependenciesplyinteractions - 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
bioconductor-package
1.08 score 67 dependenciesRAIDS - 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
bioconductor-package
1.51 score 145 dependenciesTSAR - 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
bioconductor-package
1.64 score 116 dependenciesnipalsMCIA - 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 2 months ago
bioconductor-package
1.45 score 92 dependenciesGloScope - 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
bioconductor-package
1.31 score 69 dependenciesRvisdiff - 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
bioconductor-package
0.82 score 6 dependenciesiSEEpathways - 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
bioconductor-package
1.08 score 113 dependenciesCytoPipelineGUI - 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
bioconductor-package
1.00 score 138 dependenciesgDNAx - 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
bioconductor-package
1.75 score 93 dependenciesMultiRNAflow - 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
bioconductor-package
1 stars 0.82 score 171 dependenciesiSEEde - 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
bioconductor-package
0.49 score 125 dependenciesroastgsa - 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
bioconductor-package
0.82 score 37 dependenciesHERON - 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
bioconductor-package
0.49 score 76 dependenciesRegionalST - Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data
This package analyze spatial transcriptomics data through cross-regional 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 2 months ago
bioconductor-package
0.71 score 247 dependenciesHarmonizR - 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
bioconductor-package
0.36 score 102 dependencieshicVennDiagram - 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
bioconductor-package
1.16 score 108 dependenciesorthos - `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
bioconductor-package
1.08 score 145 dependenciesCuratedAtlasQueryR - 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
bioconductor-package
0.82 score 170 dependenciesCDI - 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
bioconductor-package
0.71 score 168 dependenciesalabaster.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
bioconductor-package
0.49 score 39 dependenciesiSEEindex - 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
bioconductor-package
0.91 score 134 dependenciescfdnakit - 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
bioconductor-package
0.61 score 84 dependenciesCaDrA - 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
bioconductor-package
1.69 score 74 dependenciesgcatest - 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
bioconductor-package
1.08 score 7 dependencies 1 dependentslfa - 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
bioconductor-package
1.45 score 6 dependencies 2 dependentspartCNV - 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
bioconductor-package
0.36 score 180 dependenciesDCATS - 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
bioconductor-package
0.49 score 17 dependenciesdemuxSNP - 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
bioconductor-package
0.61 score 103 dependenciesMultimodalExperiment - 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
bioconductor-package
0.49 score 50 dependenciespfamAnalyzeR - 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
bioconductor-package
0.71 score 29 dependencies 1 dependentsTOP - 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.
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bioconductor-package
0.49 score 204 dependenciesmariner - 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
bioconductor-package
0.36 score 103 dependenciesSVMDO - 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 wilk’s 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
bioconductor-package
1.00 score 184 dependenciesBiocHail - 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 2 months ago
bioconductor-package
0.71 score 53 dependenciesOutSplice - 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
bioconductor-package
0.49 score 71 dependenciesscreenCounter - 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 2 months ago
bioconductor-package
0.91 score 38 dependenciesFeatSeekR - 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
bioconductor-package
0.36 score 43 dependenciespairedGSEA - 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
bioconductor-package
0.71 score 117 dependenciesconcordexR - Calculate the concordex coefficient
Many analysis workflows include approximation of a nearest neighbors graph followed by clustering of the graph structure. The concordex coefficient estimates the concordance between the graph and clustering results. The package 'concordexR' is an R implementation of the original concordex Python-based command line tool.
Last updated 2 months ago
bioconductor-package
0.49 score 50 dependenciesCBNplot - 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
bioconductor-package
0.61 score 142 dependenciesEDIRquery - 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
bioconductor-package
0.36 score 54 dependenciesDELocal - 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
bioconductor-package
0.71 score 75 dependencies 1 dependentsRcollectl - 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
bioconductor-package
0.71 score 34 dependenciesSpatialOmicsOverlay - 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
bioconductor-package
0.91 score 158 dependenciesSiPSiC - 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
bioconductor-package
0.71 score 29 dependenciesRarr - 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 2 months ago
bioconductor-package
1.00 score 25 dependenciesCTdata - 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
bioconductor-package
1.24 score 60 dependencies 1 dependentsTDbasedUFEadv - 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
bioconductor-package
0.36 score 211 dependenciesAHMassBank - 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
bioconductor-package
0.49 score 115 dependenciescytofQC - 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
bioconductor-package
0.49 score 231 dependenciesGeoTcgaData - 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
bioconductor-package
0.61 score 66 dependenciesMsDataHub - 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
bioconductor-package
0.82 score 60 dependenciesmagpie - 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
bioconductor-package
0.49 score 99 dependenciesflowGate - 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
bioconductor-package
0.36 score 85 dependenciesscviR - 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
bioconductor-package
0.82 score 142 dependenciesHiCool - 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
bioconductor-package
0.36 score 122 dependencieschihaya - 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
bioconductor-package
0.61 score 19 dependenciesalabaster - 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
bioconductor-package
0.49 score 110 dependenciesalabaster.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
bioconductor-package
0.91 score 83 dependencies 1 dependentsalabaster.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
bioconductor-package
1.16 score 26 dependencies 2 dependentsalabaster.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
bioconductor-package
1.00 score 62 dependencies 1 dependentsalabaster.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
bioconductor-package
0.91 score 16 dependencies 1 dependentsAnVILWorkflow - 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
bioconductor-package
0.82 score 69 dependenciesHiCExperiment - 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
bioconductor-package
1.24 score 66 dependencies 2 dependentsalabaster.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
bioconductor-package
2.76 score 0 dependencies 13 dependentsBiocHubsShiny - 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 2 months ago
bioconductor-package
0.61 score 90 dependenciesscFeatures - 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
bioconductor-package
1.51 score 240 dependenciesrifiComparative - '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
bioconductor-package
0.36 score 164 dependenciesINTACT - 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
bioconductor-package
0.49 score 24 dependenciesTDbasedUFE - 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
bioconductor-package
0.71 score 65 dependencies 1 dependentsMsBackendSql - 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 2 months ago
bioconductor-package
1.08 score 34 dependenciesBG2 - 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
bioconductor-package
0.49 score 82 dependenciesclevRvis - 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
bioconductor-package
0.36 score 113 dependenciesplanttfhunter - 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
bioconductor-package
0.36 score 29 dependenciesmicroSTASIS - 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
bioconductor-package
0.36 score 84 dependenciesmetabinR - 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
bioconductor-package
0.49 score 1 dependenciesStatial - 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
bioconductor-package
2.14 score 134 dependenciescoMET - 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
bioconductor-package
1.08 score 151 dependenciesNetActivity - 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
bioconductor-package
0.49 score 70 dependenciesFuseSOM - 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
bioconductor-package
0.61 score 125 dependenciesDNAfusion - 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
bioconductor-package
0.36 score 72 dependenciesBiocFHIR - 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
bioconductor-package
0.49 score 59 dependenciessignifinder - 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 2 months ago
bioconductor-package
1.64 score 265 dependenciescardelino - 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
bioconductor-package
0.61 score 120 dependenciesBioNAR - 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 2 months ago
bioconductor-package
1.58 score 133 dependenciesvsclust - 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 2 months ago
bioconductor-package
0.61 score 88 dependenciesggtreeDendro - 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
bioconductor-package
0.71 score 54 dependenciesepistasisGA - 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
bioconductor-package
0.36 score 107 dependenciesCircSeqAlignTk - 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
bioconductor-package
0.61 score 150 dependenciesmagrene - 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
bioconductor-package
0.36 score 9 dependenciesHiContacts - 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
bioconductor-package
0.91 score 97 dependenciesMsExperiment - 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
bioconductor-package
3.00 score 110 dependencies 15 dependentscrisprViz - 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
bioconductor-package
1.24 score 170 dependencies 2 dependentsiSEEhub - 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
bioconductor-package
0.61 score 136 dependenciesconsICA - 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
bioconductor-package
1.24 score 90 dependenciesdemuxmix - 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
bioconductor-package
0.91 score 29 dependencies 1 dependentsVDJdive - 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
bioconductor-package
0.61 score 66 dependenciesregioneReloaded - 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.
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bioconductor-package
0.61 score 96 dependenciesEasyCellType - 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
bioconductor-package
0.61 score 139 dependenciesBASiCStan - 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
bioconductor-package
0.71 score 153 dependenciescrisprVerse - 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
bioconductor-package
0.36 score 171 dependenciesSimBu - 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
bioconductor-package
1.08 score 107 dependencieszenith - 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
bioconductor-package
1.24 score 148 dependencies 1 dependentsoncoscanR - 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
bioconductor-package
0.49 score 41 dependenciesgoSorensen - 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
bioconductor-package
0.61 score 122 dependencieseds - 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
bioconductor-package
0.82 score 3 dependencies 1 dependentsRedisParam - 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
bioconductor-package
0.61 score 14 dependenciesCHETAH - 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
bioconductor-package
0.71 score 104 dependenciesHiCDOC - 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 2 months ago
bioconductor-package
1.24 score 86 dependencies 1 dependentsATACCoGAPS - Analysis Tools for scATACseq Data with CoGAPS
Provides tools for running the CoGAPS algorithm (Fertig et al, 2010) on single-cell ATAC sequencing data and analysis of the results. Can be used to perform analyses at the level of genes, motifs, TFs, or pathways. Additionally provides tools for transfer learning and data integration with single-cell RNA sequencing data.
Last updated 2 months ago
bioconductor-package
0.36 score 247 dependenciesmslp - 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
bioconductor-package
0.36 score 55 dependenciesfactR - 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
bioconductor-package
0.49 score 107 dependenciesspaSim - 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
bioconductor-package
0.61 score 85 dependencieskatdetectr - 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
bioconductor-package
0.82 score 118 dependenciessyntenet - 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 2 months ago
bioconductor-package
0.91 score 117 dependencies 1 dependentsiSEEhex - 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
bioconductor-package
1.00 score 114 dependencies 2 dependentsScreenR - 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
bioconductor-package
0.36 score 43 dependenciesRgnTX - 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
bioconductor-package
0.36 score 90 dependenciesPanViz - 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 2 months ago
bioconductor-package
0.36 score 41 dependenciesSUITOR - 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
bioconductor-package
0.36 score 37 dependenciesBiocBaseUtils - 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
bioconductor-package
7.06 score 0 dependencies 149 dependentsRAREsim - 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
bioconductor-package
0.61 score 1 dependenciescogeqc - 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
bioconductor-package
0.71 score 76 dependenciescrisprBwa - 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
bioconductor-package
0.49 score 76 dependenciesompBAM - 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
bioconductor-package
0.82 score 2 dependencies 1 dependentssSNAPPY - 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
bioconductor-package
1.24 score 100 dependenciesborealis - 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
bioconductor-package
0.61 score 107 dependenciesterraTCGAdata - 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
bioconductor-package
0.61 score 130 dependenciesGenomicInteractionNodes - 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
bioconductor-package
0.49 score 71 dependenciesepimutacions - 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
bioconductor-package
1.00 score 210 dependenciesRolDE - 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.
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bioconductor-package
0.71 score 67 dependenciesbandle - 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
bioconductor-package
0.61 score 228 dependenciespareg - 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 2 months ago
bioconductor-package
0.71 score 196 dependenciesqmtools - 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
bioconductor-package
0.61 score 151 dependenciescytoMEM - 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
bioconductor-package
0.49 score 16 dependenciestomoseqr - 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
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0.61 score 94 dependenciesprotGear - 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
bioconductor-package
0.49 score 179 dependenciessingle - Accurate consensus sequence from nanopore reads of a gene library
Accurate consensus sequence from nanopore reads of a DNA gene library. SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences of variants identified by a barcode, needing only a few reads per variant. More information in preprint doi: https://doi.org/10.1101/2020.03.25.007146.
Last updated 2 months ago
bioconductor-package
0.49 score 64 dependenciesASURAT - 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
bioconductor-package
0.71 score 48 dependenciesnnSVG - 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
bioconductor-package
1.16 score 78 dependencies 1 dependentsbiodbExpasy - biodbExpasy, a library for connecting to Expasy ENZYME database.
The biodbExpasy library provides access to Expasy ENZYME 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 or comments.
Last updated 2 months ago
bioconductor-package
0.49 score 71 dependenciesbiodbNcbi - 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
bioconductor-package
0.49 score 71 dependenciesfastreeR - 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
bioconductor-package
0.82 score 19 dependenciesbiodbNci - 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
bioconductor-package
0.49 score 71 dependenciesCBEA - 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
bioconductor-package
0.36 score 123 dependenciesrgoslin - 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
bioconductor-package
1.00 score 17 dependenciesPSMatch - 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
bioconductor-package
4.26 score 107 dependencies 36 dependentsRbwa - 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
bioconductor-package
1.00 score 0 dependencies 1 dependentsxcore - 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
bioconductor-package
0.61 score 62 dependenciesMBECS - 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
bioconductor-package
0.36 score 133 dependenciesUCell - 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
bioconductor-package
1.69 score 42 dependencies 2 dependentscellxgenedp - 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
bioconductor-package
1.24 score 57 dependenciesMuData - 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
bioconductor-package
0.61 score 54 dependenciesMsBackendMsp - 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.
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bioconductor-package
0.91 score 21 dependenciescrisprBowtie - 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
bioconductor-package
1.51 score 76 dependencies 4 dependentsMotif2Site - 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.
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bioconductor-package
0.49 score 116 dependenciesbeer - 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
bioconductor-package
0.61 score 78 dependencieslineagespot - 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
bioconductor-package
1.16 score 74 dependenciesPanomiR - 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.
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bioconductor-package
0.61 score 152 dependenciesdestiny - Creates diffusion maps
Create and plot diffusion maps.
Last updated 2 months ago
bioconductor-package
3.31 score 109 dependenciesMSA2dist - 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.
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bioconductor-package
1.24 score 57 dependencies 1 dependentsRCX - 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
bioconductor-package
0.82 score 14 dependencies 1 dependentsOGRE - 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
bioconductor-package
0.49 score 163 dependenciescomapr - 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.
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bioconductor-package
0.61 score 158 dependenciescrisprScore - 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.
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bioconductor-package
1.75 score 72 dependencies 4 dependentsBOBaFIT - 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.
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bioconductor-package
0.61 score 168 dependenciescrisprBase - 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
bioconductor-package
1.90 score 27 dependencies 6 dependentsrprimer - 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
bioconductor-package
0.61 score 84 dependenciesMouseFM - 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
bioconductor-package
0.61 score 86 dependenciessccomp - 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.
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bioconductor-package
1.69 score 109 dependenciesbiodbHmdb - 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.
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bioconductor-package
0.61 score 72 dependenciespengls - 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
bioconductor-package
0.36 score 19 dependenciesCellBarcode - 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 2 months ago
bioconductor-package
1.08 score 92 dependenciesRiboCrypt - 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
bioconductor-package
0.82 score 158 dependenciestxcutr - 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
bioconductor-package
0.82 score 93 dependenciesGeoDiff - 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
bioconductor-package
0.82 score 152 dependenciesscatterHatch - 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
bioconductor-package
0.61 score 35 dependenciesbiodbKegg - biodbKegg, a library for connecting to the KEGG Database
The biodbKegg library is an extension of the biodb framework package that provides access to the KEGG databases Compound, Enzyme, Genes, Module, Orthology and Reaction. It allows to retrieve entries by their accession numbers. Web services like "find", "list" and "findExactMass" are also available. Some functions for navigating along the pathways have also been implemented.
Last updated 2 months ago
bioconductor-package
0.61 score 71 dependenciesdeconvR - 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
bioconductor-package
0.71 score 165 dependenciesmiaSim - 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
bioconductor-package
1.08 score 74 dependenciesMSstatsLiP - 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
bioconductor-package
0.71 score 183 dependenciesCyTOFpower - 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
bioconductor-package
0.49 score 221 dependenciesCogito - 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
bioconductor-package
0.49 score 105 dependenciesbiodbUniprot - 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
bioconductor-package
0.49 score 71 dependenciescliProfiler - 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
bioconductor-package
0.49 score 78 dependenciesnullranges - 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
bioconductor-package
1.45 score 85 dependencies 1 dependentsTRESS - 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
bioconductor-package
0.91 score 68 dependencies 1 dependentsMicrobiomeProfiler - 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
bioconductor-package
0.82 score 151 dependenciessparrow - 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 2 months ago
bioconductor-package
1.08 score 136 dependencies 1 dependentsCexoR - 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
bioconductor-package
1.00 score 98 dependenciesscTreeViz - 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
bioconductor-package
0.82 score 246 dependenciesbiodbChebi - 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
bioconductor-package
0.82 score 71 dependencies 1 dependentsggmsa - 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 months ago
bioconductor-package
1.38 score 106 dependencies 2 dependentsatena - 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
bioconductor-package
1.00 score 91 dependenciesorthogene - 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
bioconductor-package
1.00 score 142 dependencies 1 dependentstransformGamPoi - 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
bioconductor-package
0.49 score 44 dependenciesscReClassify - 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
bioconductor-package
0.61 score 34 dependenciestripr - 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
bioconductor-package
1.00 score 90 dependenciesrGenomeTracks - 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
bioconductor-package
0.49 score 75 dependenciesmetapone - 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
bioconductor-package
0.49 score 51 dependenciesscAnnotatR - 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
bioconductor-package
0.82 score 205 dependenciesProteoDisco - 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
bioconductor-package
0.71 score 90 dependenciestanggle - 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
bioconductor-package
0.71 score 58 dependenciessvaRetro - 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
bioconductor-package
0.82 score 84 dependenciesbugsigdbr - 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
bioconductor-package
1.58 score 46 dependenciesggspavis - 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
bioconductor-package
1.00 score 80 dependenciesspatialDE - 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
bioconductor-package
1.00 score 91 dependenciestraviz - 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
bioconductor-package
0.61 score 83 dependenciesgenomicInstability - 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
bioconductor-package
0.49 score 94 dependenciesveloviz - 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
bioconductor-package
0.71 score 16 dependenciesGEOexplorer - 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
bioconductor-package
0.91 score 211 dependenciesscanMiRApp - 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
bioconductor-package
1.00 score 151 dependenciesspatzie - 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
bioconductor-package
0.61 score 174 dependenciescfDNAPro - 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
bioconductor-package
0.49 score 88 dependenciesmitoClone2 - 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
bioconductor-package
0.49 score 97 dependenciescageminer - 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
bioconductor-package
0.71 score 206 dependenciesFLAMES - 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 2 months ago
bioconductor-package
2.42 score 247 dependenciesNeuCA - 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
bioconductor-package
0.82 score 94 dependenciesscanMiR - 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
bioconductor-package
1.45 score 60 dependencies 1 dependentssvaNUMT - 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
bioconductor-package
1.08 score 84 dependenciescsdR - 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
bioconductor-package
0.49 score 105 dependenciesmethylclock - 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
bioconductor-package
0.82 score 286 dependenciesFindIT2 - 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
bioconductor-package
0.61 score 111 dependenciessegmenter - 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
bioconductor-package
0.82 score 156 dependenciesdStruct - 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
bioconductor-package
0.61 score 38 dependenciesNanoTube - 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.
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bioconductor-package
0.61 score 48 dependenciesm6Aboost - 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
bioconductor-package
0.61 score 161 dependenciesDelayedTensor - 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
bioconductor-package
0.49 score 40 dependenciesspiky - 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
bioconductor-package
0.82 score 85 dependenciesReactomeGraph4R - 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.
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bioconductor-package
0.61 score 63 dependenciesGenomicSuperSignature - 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
bioconductor-package
0.82 score 162 dependenciesepigraHMM - 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
bioconductor-package
0.61 score 126 dependenciesHubPub - 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.
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bioconductor-package
1.00 score 69 dependenciesvissE - 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.
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bioconductor-package
0.71 score 133 dependenciesepialleleR - 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 methylation patterns and assess allele specificity of methylation.
Last updated 2 months ago
bioconductor-package
1.51 score 72 dependenciesHGC - 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.
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bioconductor-package
0.61 score 41 dependenciescosmosR - 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.
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bioconductor-package
1.08 score 101 dependenciesdiffUTR - 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.
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bioconductor-package
0.49 score 135 dependenciescbpManager - 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
bioconductor-package
0.91 score 81 dependenciesMQmetrics - Quality Control of Protemics Data
The package MQmetrics (MaxQuant metrics) provides a workflow to analyze the quality and reproducibility of your proteomics mass spectrometry analysis from MaxQuant.Input data are extracted from several MaxQuant output tables and produces a pdf report. It includes several visualization tools to check numerous parameters regarding the quality of the runs. It also includes two functions to visualize the iRT peptides from Biognosys in case they were spiked in the samples.
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bioconductor-package
0.49 score 105 dependenciesbiodb - 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
bioconductor-package
2.22 score 70 dependencies 8 dependentsfgga - 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
bioconductor-package
0.61 score 55 dependenciesDExMA - 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
bioconductor-package
0.91 score 112 dependenciesmiloR - 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
bioconductor-package
1.38 score 105 dependenciessupersigs - 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
bioconductor-package
0.61 score 107 dependenciesawst - 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
bioconductor-package
0.61 score 28 dependenciesquantiseqr - 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 2 months ago
bioconductor-package
1.08 score 65 dependencies 1 dependentsRbec - 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
bioconductor-package
0.49 score 96 dependenciesDelayedRandomArray - 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
bioconductor-package
0.91 score 18 dependencies 1 dependentsgranulator - 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
bioconductor-package
0.49 score 116 dependenciesflowVS - 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
bioconductor-package
1.08 score 93 dependenciesCGEN - 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
bioconductor-package
1.08 score 4 dependenciesinteracCircos - 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
bioconductor-package
0.49 score 30 dependenciestricycle - 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
bioconductor-package
0.71 score 118 dependenciesEWCE - 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
bioconductor-package
1.45 score 190 dependenciescellmigRation - 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
bioconductor-package
0.82 score 129 dependenciesCNViz - 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
bioconductor-package
0.49 score 151 dependenciescyanoFilter - 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
bioconductor-package
0.71 score 128 dependenciesmirTarRnaSeq - 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
bioconductor-package
0.61 score 49 dependenciesCytoGLMM - 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
bioconductor-package
0.82 score 158 dependencies 1 dependentsbarcodetrackR - 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
bioconductor-package
0.61 score 94 dependenciescondiments - 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 2 months ago
bioconductor-package
0.49 score 161 dependenciesairpart - 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.
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bioconductor-package
0.61 score 134 dependenciesdrugTargetInteractions - 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.
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bioconductor-package
0.61 score 100 dependenciesfedup - 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
bioconductor-package
0.49 score 72 dependenciesCIMICE - 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
bioconductor-package
0.49 score 85 dependenciesmemes - 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
bioconductor-package
0.49 score 103 dependenciesdir.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
bioconductor-package
4.12 score 1 dependencies 34 dependentsmethylscaper - 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
bioconductor-package
1.08 score 99 dependenciesCelliD - 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
bioconductor-package
0.71 score 191 dependenciesMsBackendMgf - 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 2 months ago
bioconductor-package
0.91 score 21 dependenciesCTDquerier - 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
bioconductor-package
1.16 score 62 dependenciesPhIPData - 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
bioconductor-package
0.82 score 65 dependencies 1 dependentsComPrAn - 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
bioconductor-package
0.61 score 99 dependenciesModCon - 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
bioconductor-package
0.49 score 1 dependenciesdce - 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 2 months ago
bioconductor-package
0.82 score 233 dependencieshca - 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.
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bioconductor-package
0.91 score 77 dependenciesMsBackendMassbank - 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
bioconductor-package
0.82 score 22 dependenciesPhenoGeneRanker - 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
bioconductor-package
0.61 score 24 dependenciesMAGAR - 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 2 months ago
bioconductor-package
0.61 score 185 dependenciessatuRn - 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
bioconductor-package
0.91 score 67 dependencies 1 dependentsSummix - 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 2 months ago
bioconductor-package
1.00 score 67 dependenciesMACSr - 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
bioconductor-package
0.91 score 70 dependenciesfobitools - 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 2 months ago
bioconductor-package
0.71 score 117 dependenciesMetaboCoreUtils - 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
bioconductor-package
4.13 score 16 dependencies 30 dependentsTrajectoryUtils - 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
bioconductor-package
2.35 score 38 dependencies 9 dependentsSOMNiBUS - 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 2 months ago
bioconductor-package
1.08 score 132 dependenciesGeomxTools - 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
bioconductor-package
1.90 score 129 dependencies 3 dependentsRiboDiPA - 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 2 months ago
bioconductor-package
0.71 score 140 dependenciesNanoStringNCTools - 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
bioconductor-package
2.27 score 79 dependencies 4 dependentsplanet - 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
bioconductor-package
1.08 score 16 dependencies 1 dependentsInteractiveComplexHeatmap - 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
bioconductor-package
1.51 score 71 dependencies 3 dependentssampleClassifier - Sample Classifier
The package is designed to classify microarray RNA-seq gene expression profiles.
Last updated 2 months ago
bioconductor-package
1.08 score 85 dependenciesScaledMatrix - 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
bioconductor-package
6.12 score 14 dependencies 97 dependentsSCArray - 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 2 months ago
bioconductor-package
1.38 score 47 dependencies 1 dependentsramr - Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite 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.
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bioconductor-package
0.61 score 64 dependenciesBumpyMatrix - 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
bioconductor-package
2.50 score 5 dependencies 11 dependentsCAEN - 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
bioconductor-package
1.58 score 29 dependenciesmumosa - 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
bioconductor-package
0.61 score 75 dependenciesGEOfastq - 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.
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bioconductor-package
0.49 score 32 dependenciescenscyt - 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
bioconductor-package
0.49 score 168 dependenciesnempi - 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
bioconductor-package
0.71 score 104 dependenciesSplicingFactory - 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
bioconductor-package
0.82 score 28 dependenciesflowGraph - 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
bioconductor-package
0.49 score 73 dependenciesbnem - 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).
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bioconductor-package
0.49 score 169 dependenciesReactomeContentService4R - 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
bioconductor-package
1.00 score 16 dependencies 1 dependentsmetapod - 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
bioconductor-package
4.58 score 1 dependencies 44 dependentsshinyepico - 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
bioconductor-package
0.49 score 196 dependenciesmoanin - 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.
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bioconductor-package
0.61 score 87 dependenciesGSgalgoR - 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.
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bioconductor-package
0.61 score 14 dependenciesNewWave - 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.
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bioconductor-package
0.61 score 45 dependenciesscRepertoire - 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 months ago
bioconductor-package
1.31 score 110 dependenciesCellaRepertorium - Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
Methods to cluster and analyze high-throughput single cell immune cell repertoires, especially from the 10X Genomics VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006). Methods to visualize and analyze paired heavy-light chain data. Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.
Last updated 2 months ago
bioconductor-package
0.82 score 47 dependenciesAnVILBilling - 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
bioconductor-package
0.61 score 90 dependenciesmegadepth - 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 2 months ago
bioconductor-package
0.61 score 77 dependenciesSCFA - 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
bioconductor-package
0.36 score 46 dependenciesbambu - 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
bioconductor-package
1.45 score 86 dependencies 1 dependentsMOGAMUN - 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
bioconductor-package
0.71 score 59 dependenciesMOFA2 - 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
bioconductor-package
1.24 score 82 dependenciesAnVILPublish - 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
bioconductor-package
1.24 score 79 dependenciesExperimentSubset - 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
bioconductor-package
0.61 score 83 dependenciesbiocthis - 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 2 months ago
bioconductor-package
1.80 score 38 dependencies 1 dependentsSpatialDecon - 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.
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bioconductor-package
1.31 score 136 dependenciesrecount3 - 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 2 months ago
bioconductor-package
1.31 score 85 dependenciesRnaSeqSampleSize - 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
bioconductor-package
1.00 score 191 dependenciesmicrobiomeExplorer - 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
bioconductor-package
0.49 score 181 dependenciesscp - 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.
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bioconductor-package
1.31 score 107 dependenciesrnaEditr - 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
bioconductor-package
0.49 score 127 dependenciescustomCMPdb - 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
bioconductor-package
0.71 score 104 dependenciesBayesSpace - 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
bioconductor-package
1.00 score 145 dependencies 1 dependentsspatialHeatmap - spatialHeatmap
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.
Last updated 2 months ago
bioconductor-package
1.38 score 163 dependenciesChromSCape - 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
bioconductor-package
0.91 score 202 dependenciesMSPrep - 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
bioconductor-package
0.82 score 144 dependenciesInformeasure - 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
bioconductor-package
0.61 score 1 dependenciesMSstatsPTM - 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.
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bioconductor-package
1.69 score 106 dependencies 2 dependentsSeqGate - 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
bioconductor-package
0.49 score 29 dependenciesPhosR - 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
bioconductor-package
0.91 score 136 dependenciesmsImpute - 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).
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bioconductor-package
0.49 score 90 dependenciespageRank - 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
bioconductor-package
0.36 score 119 dependenciesTileDBArray - 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
bioconductor-package
0.71 score 26 dependenciesnearBynding - 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.
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bioconductor-package
0.49 score 104 dependenciesrsemmed - 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
bioconductor-package
0.49 score 22 dependenciesFilterFFPE - 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.
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bioconductor-package
0.49 score 34 dependenciesncRNAtools - 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.
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bioconductor-package
0.36 score 45 dependenciesperiodicDNA - 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.
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bioconductor-package
0.61 score 77 dependenciesrecountmethylation - 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.
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bioconductor-package
0.82 score 141 dependenciesRfastp - 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
bioconductor-package
0.61 score 36 dependenciesidpr - 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
bioconductor-package
0.71 score 50 dependenciesVplotR - 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.
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bioconductor-package
0.82 score 74 dependenciesrebook - 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
bioconductor-package
0.61 score 36 dependenciesNebulosa - 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.
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bioconductor-package
0.91 score 88 dependenciessnifter - 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
bioconductor-package
0.91 score 18 dependenciesuncoverappLib - 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.
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bioconductor-package
0.49 score 180 dependenciesOmixer - 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.
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bioconductor-package
0.49 score 46 dependenciesggtreeExtra - 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
bioconductor-package
1.16 score 55 dependencies 1 dependentsMesKit - 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
bioconductor-package
1 stars 1.24 score 92 dependencies 1 dependentsescape - 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
bioconductor-package
1.24 score 163 dependenciesinfinityFlow - 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
bioconductor-package
0.61 score 33 dependenciesbluster - 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
bioconductor-package
4.66 score 25 dependencies 45 dependentsMultiBaC - 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.
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bioconductor-package
0.49 score 99 dependencieswpm - 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.
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bioconductor-package
0.49 score 100 dependenciesscCB2 - 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.
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bioconductor-package
0.49 score 186 dependenciesGWENA - 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
bioconductor-package
0.61 score 132 dependenciesRtpca - 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
bioconductor-package
0.49 score 42 dependenciesmultiGSEA - 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 2 months ago
bioconductor-package
0.91 score 113 dependenciesToxicoGx - 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
bioconductor-package
1.16 score 135 dependenciesPeacoQC - 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.
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bioconductor-package
1.75 score 74 dependencies 3 dependentsRegEnrich - 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.
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bioconductor-package
1.08 score 145 dependenciesSPsimSeq - 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.
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bioconductor-package
1.24 score 134 dependencies 1 dependentsgetDEE2 - 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).
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bioconductor-package
0.49 score 29 dependenciesmulticrispr - 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.
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bioconductor-package
1.00 score 163 dependenciesDegNorm - 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
bioconductor-package
0.71 score 152 dependenciessimplifyEnrichment - 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
bioconductor-package
0.82 score 69 dependenciesflowCut - 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
bioconductor-package
0.91 score 97 dependenciesTADCompare - 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.
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bioconductor-package
0.82 score 124 dependenciessangeranalyseR - 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.
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bioconductor-package
1.08 score 115 dependenciescBioPortalData - 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.
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bioconductor-package
2.35 score 133 dependencies 4 dependentsLACE - 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
bioconductor-package
1.08 score 156 dependenciessnapcount - 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).
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bioconductor-package
0.82 score 39 dependenciesoptimalFlow - optimalFlow
Optimal-transport techniques applied to supervised flow cytometry gating.
Last updated 2 months ago
bioconductor-package
0.49 score 86 dependenciesmetaseqR2 - 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
bioconductor-package
1.16 score 227 dependenciesSingleCellSignalR - 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
bioconductor-package
0.91 score 94 dependencies 1 dependentsSynExtend - 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 2 months ago
bioconductor-package
1.16 score 35 dependenciesscry - 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.
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bioconductor-package
0.82 score 46 dependenciesCARNIVAL - 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
bioconductor-package
1.45 score 57 dependencies 1 dependentsMOMA - 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
bioconductor-package
0.61 score 95 dependenciesROSeq - 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
bioconductor-package
0.49 score 7 dependenciesmethylSig - 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.
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bioconductor-package
0.61 score 80 dependenciesscClassify - 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
bioconductor-package
1.45 score 147 dependenciesOpenStats - 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 2 months ago
bioconductor-package
0.82 score 115 dependenciesrandRotation - 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
bioconductor-package
0.49 score 2 dependenciesrfaRm - 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
bioconductor-package
0.91 score 38 dependenciesspqn - 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
bioconductor-package
0.61 score 54 dependenciesCiteFuse - 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
bioconductor-package
0.71 score 155 dependenciesiSEEu - 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
bioconductor-package
1.24 score 115 dependencies 1 dependentsMsCoreUtils - 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
bioconductor-package
5.32 score 6 dependencies 61 dependentsMicrobiotaProcess - 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
bioconductor-package
1.75 score 103 dependenciestimeOmics - 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
bioconductor-package
1.16 score 61 dependenciesExploreModelMatrix - 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 2 months ago
bioconductor-package
0.82 score 78 dependenciesMatrixGenerics - 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
bioconductor-package
12.75 score 1 dependencies 1237 dependentsGPA - 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
bioconductor-package
0.49 score 68 dependenciespeco - 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
bioconductor-package
0.82 score 110 dependenciesHIPPO - 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
bioconductor-package
0.49 score 75 dependenciesROCpAI - 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
bioconductor-package
0.49 score 35 dependenciescombi - 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
bioconductor-package
0.71 score 94 dependenciesDune - 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
bioconductor-package
0.61 score 88 dependenciescmapR - 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
bioconductor-package
1.80 score 38 dependenciesEpiTxDb - 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
bioconductor-package
0.82 score 112 dependencieseisaR - 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
bioconductor-package
1.08 score 33 dependenciesRNAAgeCalc - 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
bioconductor-package
0.36 score 157 dependenciesrhdf5filters - 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
bioconductor-package
8.01 score 1 dependencies 220 dependentsTAPseq - 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
bioconductor-package
0.82 score 82 dependenciesscTHI - 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
bioconductor-package
0.61 score 11 dependenciesribor - 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
bioconductor-package
0.61 score 43 dependenciesreceptLoss - 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
bioconductor-package
0.82 score 61 dependenciesrrvgo - Reduce + Visualize GO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Last updated 2 months ago
bioconductor-package
1.31 score 98 dependencies 1 dependentsribosomeProfilingQC - 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
bioconductor-package
1.00 score 181 dependenciesVaSP - 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
bioconductor-package
0.61 score 82 dependenciesbasilisk.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
bioconductor-package
4.15 score 2 dependencies 32 dependentsfrenchFISH - 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
bioconductor-package
0.49 score 63 dependenciesclustifyr - 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
bioconductor-package
1.45 score 89 dependenciesbasilisk - 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
bioconductor-package
4.20 score 15 dependencies 31 dependentsTreeAndLeaf - 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
bioconductor-package
0.61 score 24 dependenciesMEAT - 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
bioconductor-package
0.61 score 165 dependenciesGeneTonic - 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 months ago
bioconductor-package
1.38 score 157 dependencies 1 dependentsstruct - 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
bioconductor-package
1.58 score 44 dependencies 2 dependentsDIAlignR - 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 2 months ago
bioconductor-package
0.91 score 71 dependenciesDAMEfinder - 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
bioconductor-package
0.82 score 112 dependenciesSimFFPE - 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
bioconductor-package
0.49 score 50 dependenciesreconsi - 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
bioconductor-package
0.61 score 82 dependenciesrSWeeP - Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
The SWeeP method was developed to favor the analizes between amino acids sequences and to assist alignment free phylogenetic studies. This method is based on the concept of sparse words, which is applied in the scan of biological sequences and its the conversion in a matrix of ocurrences. Aiming the generation of low dimensional matrices of Amino Acid Sequence occurrences.
Last updated 2 months ago
bioconductor-package
0.49 score 1 dependenciespackFinder - 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
bioconductor-package
0.49 score 26 dependenciesBgeeCall - 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
bioconductor-package
1.00 score 103 dependencieseasyreporting - 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
bioconductor-package
0.49 score 37 dependenciesdearseq - 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
bioconductor-package
1.38 score 50 dependencies 1 dependentsEnMCB - 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
bioconductor-package
0.49 score 119 dependenciesbiobtreeR - 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
bioconductor-package
0.61 score 16 dependenciesCSSQ - 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
bioconductor-package
0.49 score 87 dependenciesNPARC - 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
bioconductor-package
0.61 score 32 dependenciesPathNet - 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
bioconductor-package
1.16 score 0 dependenciesselectKSigs - 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
bioconductor-package
0.49 score 107 dependenciesBiocSet - 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
bioconductor-package
1.64 score 55 dependencies 4 dependentssignatureSearch - 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
bioconductor-package
1.08 score 168 dependencies 1 dependentsbrainflowprobes - Plots and annotation for choosing BrainFlow target probe sequence
Use these functions to characterize genomic regions for BrainFlow target probe design.
Last updated 2 months ago
bioconductor-package
0.71 score 180 dependenciesscTGIF - 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
bioconductor-package
0.49 score 139 dependenciesmethrix - 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
bioconductor-package
1.38 score 83 dependenciesMACSQuantifyR - 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
bioconductor-package
0.49 score 77 dependenciesoppti - 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
bioconductor-package
0.49 score 119 dependenciesscPCA - 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
bioconductor-package
0.91 score 64 dependenciesDEWSeq - 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
bioconductor-package
1.00 score 70 dependenciesbiscuiteer - 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
bioconductor-package
1.38 score 170 dependenciesMBQN - 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
bioconductor-package
0.71 score 102 dependenciesschex - 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
bioconductor-package
1.64 score 79 dependencies 2 dependentswaddR - 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
bioconductor-package
0.82 score 94 dependenciestarget - 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
bioconductor-package
0.61 score 45 dependenciesssPATHS - 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.
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bioconductor-package
0.49 score 109 dependenciesblacksheepr - 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
bioconductor-package
0.49 score 123 dependenciesgscreend - 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
bioconductor-package
0.71 score 51 dependenciesCNVfilteR - 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
bioconductor-package
0.71 score 138 dependenciesmethylCC - 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
bioconductor-package
1.24 score 145 dependenciesGmicR - 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
bioconductor-package
0.49 score 145 dependenciespeakPantheR - 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.
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bioconductor-package
0.91 score 141 dependenciesSpaniel - 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
bioconductor-package
0.71 score 203 dependencieslionessR - 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
bioconductor-package
0.91 score 28 dependenciesflowSpecs - 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.
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bioconductor-package
0.49 score 51 dependenciesReactomeGSA - 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 2 months ago
bioconductor-package
1.69 score 54 dependenciesdebCAM - 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
bioconductor-package
0.91 score 108 dependenciesSEtools - 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
bioconductor-package
0.61 score 118 dependenciesidr2d - 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
bioconductor-package
0.49 score 61 dependenciesmicrobiomeDASim - 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
bioconductor-package
0.49 score 93 dependenciesQtlizer - 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
bioconductor-package
0.61 score 18 dependenciesdeltaCaptureC - 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
bioconductor-package
0.71 score 67 dependenciescalm - 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
bioconductor-package
0.49 score 4 dependenciesmuscat - 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
bioconductor-package
1.16 score 168 dependenciesbrendaDb - The BRENDA Enzyme Database
R interface for importing and analyzing enzyme information from the BRENDA database.
Last updated 2 months ago
bioconductor-package
0.49 score 51 dependenciesSigsPack - 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
bioconductor-package
0.61 score 71 dependenciesGenomicOZone - 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
bioconductor-package
0.49 score 165 dependenciesfcScan - 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
bioconductor-package
0.61 score 75 dependenciesAPAlyzer - 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
bioconductor-package
0.61 score 113 dependenciesAlphaBeta - 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
bioconductor-package
0.71 score 85 dependenciesIgGeneUsage - 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
bioconductor-package
1.95 score 85 dependenciesscBFA - 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
bioconductor-package
0.61 score 194 dependenciesproDA - 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
bioconductor-package
1.24 score 30 dependencies 1 dependentsncGTW - 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
bioconductor-package
0.49 score 137 dependenciesMaaslin2 - "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
bioconductor-package
1.85 score 112 dependencies 3 dependentsHiLDA - 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
bioconductor-package
0.91 score 105 dependencies 1 dependentsscGPS - 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
bioconductor-package
0.61 score 117 dependenciescircRNAprofiler - 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
bioconductor-package
0.82 score 133 dependenciesAWFisher - 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
bioconductor-package
0.49 score 6 dependenciesgemini - 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
bioconductor-package
0.49 score 75 dependenciesGOTHiC - 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
bioconductor-package
3.26 score 87 dependenciesRNAmodR.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
bioconductor-package
0.61 score 159 dependenciesTOAST - 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
bioconductor-package
1.31 score 95 dependencies 3 dependentsRNAmodR.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
bioconductor-package
0.49 score 158 dependenciesRNAmodR.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
bioconductor-package
1 stars 0.61 score 158 dependenciesRNAmodR - 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
bioconductor-package
1.45 score 157 dependencies 3 dependentsSQLDataFrame - 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
bioconductor-package
1.08 score 31 dependenciesVennDetail - 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
bioconductor-package
0.61 score 41 dependenciesTreeSummarizedExperiment - 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
bioconductor-package
2.94 score 70 dependencies 15 dependentsStructuralVariantAnnotation - 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
bioconductor-package
1.38 score 83 dependencies 2 dependentsPAST - 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
bioconductor-package
0.61 score 86 dependenciesGladiaTOX - 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
bioconductor-package
0.71 score 59 dependenciesSubCellBarCode - 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
bioconductor-package
0.49 score 129 dependenciescelda - 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
bioconductor-package
2.18 score 130 dependencies 2 dependentsTPP2D - 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
bioconductor-package
0.49 score 54 dependenciesmetagene2 - 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
bioconductor-package
1.00 score 84 dependenciesSynMut - 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
bioconductor-package
0.49 score 36 dependenciesnanotatoR -
Last updated 2 months ago
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
bioconductor-package
0.61 score 53 dependenciesscMerge - 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
bioconductor-package
1.16 score 178 dependencies 1 dependentsdcanr - 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
bioconductor-package
0.82 score 27 dependencies 1 dependentsCopyNumberPlots - 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
bioconductor-package
1.31 score 135 dependencies 2 dependentsADAMgui - 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
bioconductor-package
0.61 score 149 dependenciesscRecover - 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
bioconductor-package
0.49 score 36 dependenciesRepViz - 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
bioconductor-package
0.71 score 74 dependenciesssrch - a simple search engine
Demonstrate tokenization and a search gadget for collections of CSV files.
Last updated 2 months ago
bioconductor-package
0.49 score 41 dependenciesBANDITS - 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
bioconductor-package
0.82 score 74 dependencies 1 dependentsNBAMSeq - 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
bioconductor-package
0.49 score 84 dependenciesDiscoRhythm - 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
bioconductor-package
0.71 score 149 dependenciesngsReports - 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
bioconductor-package
1.38 score 90 dependenciesmbkmeans - 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
bioconductor-package
1.31 score 79 dependencies 2 dependentsCellMixS - 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
bioconductor-package
0.82 score 109 dependenciessurvtype - 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
bioconductor-package
0.49 score 126 dependenciesbatchelor - 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
bioconductor-package
2.00 score 58 dependencies 6 dependentsGNET2 - 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
bioconductor-package
0.61 score 99 dependenciesDeMixT - 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
bioconductor-package
1.08 score 137 dependenciesqsmooth - 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
bioconductor-package
0.82 score 118 dependenciesprojectR - 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
bioconductor-package
2.09 score 93 dependencies 1 dependentsStructstrings - 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
bioconductor-package
1.64 score 26 dependencies 4 dependentsRcwlPipelines - 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
bioconductor-package
1.08 score 115 dependencies 1 dependentsqckitfastq - 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
bioconductor-package
0.71 score 40 dependenciesPrInCE - 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
bioconductor-package
0.61 score 165 dependencieshypeR - An R Package For Geneset Enrichment Workflows
An R Package for Geneset Enrichment Workflows.
Last updated 2 months ago
bioconductor-package
1.58 score 93 dependenciesCellBench - 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
bioconductor-package
2.18 score 73 dependenciesXeva - 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 2 months ago
bioconductor-package
1.00 score 159 dependenciesscds - 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
bioconductor-package
1.08 score 49 dependencies 1 dependentsSpectralTAD - 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
bioconductor-package
0.82 score 78 dependenciesfishpond - 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
bioconductor-package
1.31 score 62 dependenciesalevinQC - 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 2 months ago
bioconductor-package
0.82 score 93 dependenciesatSNP - 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
bioconductor-package
0.71 score 158 dependenciesCNVRanger - 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
bioconductor-package
1.24 score 64 dependenciesrmelting - 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
bioconductor-package
0.71 score 3 dependenciesdivergence - 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
bioconductor-package
0.49 score 28 dependenciesMelissa - 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
bioconductor-package
1.51 score 102 dependenciesSMAD - 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
bioconductor-package
0.61 score 24 dependenciestopconfects - 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 2 months ago
bioconductor-package
1.16 score 29 dependencies 2 dependentsadductomicsR - 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
bioconductor-package
0.49 score 127 dependenciesRhisat2 - 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 2 months ago
bioconductor-package
1.16 score 96 dependencies 1 dependentsOVESEG - 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
bioconductor-package
0.36 score 41 dependenciesPAIRADISE - 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
bioconductor-package
0.71 score 38 dependenciesRCM - 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
bioconductor-package
0.61 score 89 dependenciesCluMSID - 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
bioconductor-package
0.82 score 156 dependenciesgraper - 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
bioconductor-package
0.49 score 33 dependenciesSpatialCPie - 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
bioconductor-package
0.61 score 115 dependenciesVCFArray - 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
bioconductor-package
0.49 score 71 dependenciesDelayedDataFrame - 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
bioconductor-package
0.91 score 14 dependencies 1 dependentsdecompTumor2Sig - 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
bioconductor-package
0.82 score 103 dependencies 1 dependentsIsoCorrectoRGUI - 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
bioconductor-package
0.61 score 37 dependenciesscTensor - 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
bioconductor-package
0.61 score 223 dependenciesADAM - 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
bioconductor-package
0.82 score 85 dependencies 1 dependentsPepsNMR - 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
bioconductor-package
1.00 score 38 dependencies 1 dependentsLoomExperiment - 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
bioconductor-package
1.24 score 42 dependencies 1 dependentsuniversalmotif - 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 2 months ago
bioconductor-package
2.83 score 50 dependencies 10 dependentsabseqR - 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
bioconductor-package
0.61 score 101 dependenciesartMS - 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
bioconductor-package
1.08 score 136 dependenciesAssessORF - 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
bioconductor-package
0.71 score 21 dependenciestRNAdbImport - 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
bioconductor-package
1.16 score 54 dependencies 1 dependentsconsensusDE - 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
bioconductor-package
1.00 score 140 dependenciesWrench - 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
bioconductor-package
2.50 score 5 dependencies 10 dependentscTRAP - 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
bioconductor-package
0.71 score 150 dependenciesQSutils - 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
bioconductor-package
1.58 score 27 dependencies 1 dependentstRNA - 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
bioconductor-package
1.64 score 50 dependencies 3 dependentsHiCBricks - 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
bioconductor-package
1.08 score 79 dependencies 1 dependentstransite - 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
bioconductor-package
0.71 score 52 dependencieslevi - 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
bioconductor-package
0.61 score 92 dependenciesbayNorm - Single-cell RNA sequencing data normalization
bayNorm is used for normalizing single-cell RNA-seq data.
Last updated 2 months ago
bioconductor-package
0.91 score 50 dependenciesKinSwingR - 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
bioconductor-package
0.61 score 29 dependenciesMPRAnalyze - 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
bioconductor-package
0.82 score 46 dependenciesAffiXcan - 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
bioconductor-package
0.61 score 58 dependenciescicero - 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
bioconductor-package
0.82 score 173 dependenciescountsimQC - 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 2 months ago
bioconductor-package
0.82 score 123 dependenciesbreakpointR - 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
bioconductor-package
0.82 score 73 dependenciesERSSA - 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
bioconductor-package
0.82 score 79 dependenciesSIMD - 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
bioconductor-package
0.82 score 7 dependenciesNormalyzerDE - 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
bioconductor-package
0.91 score 106 dependenciesprimirTSS - 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
bioconductor-package
0.82 score 186 dependenciesmiRSM - 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
bioconductor-package
1.00 score 250 dependenciesHPAanalyze - 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
bioconductor-package
0.61 score 37 dependenciesREBET - 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 2 months ago
bioconductor-package
0.91 score 9 dependenciesEnhancedVolcano - 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
bioconductor-package
1.24 score 30 dependencies 1 dependentsnuCpos - 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
bioconductor-package
0.91 score 0 dependenciesSCBN - 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
bioconductor-package
1.00 score 0 dependencies 1 dependentscelaref - 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
bioconductor-package
0.82 score 74 dependencieshierinf - 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
bioconductor-package
0.61 score 11 dependenciesconsensus - 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
bioconductor-package
1.80 score 7 dependenciescoRdon - 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
bioconductor-package
2.14 score 53 dependencies 1 dependentsstrandCheckR - 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
bioconductor-package
0.91 score 112 dependenciesLRBaseDbi - DBI to construct LRBase-related package
Interface to construct LRBase package (LRBase.XXX.eg.db).
Last updated 2 months ago
bioconductor-package
0.82 score 38 dependenciesMetID - 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
bioconductor-package
0.61 score 125 dependenciesscruff - 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
bioconductor-package
1.00 score 174 dependenciesACE - 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
bioconductor-package
0.71 score 78 dependenciesOUTRIDER - 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
bioconductor-package
1.69 score 160 dependencies 1 dependentsappreci8R - 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
bioconductor-package
0.91 score 156 dependenciesmethylGSA - 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
bioconductor-package
0.61 score 209 dependenciesipdDb - 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
bioconductor-package
0.71 score 61 dependenciesBiocNeighbors - 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 2 months ago
bioconductor-package
5.75 score 15 dependencies 80 dependentsqPLEXanalyzer - Tools for quantitative proteomics data analysis
Tools for TMT based quantitative proteomics data analysis.
Last updated 2 months ago
bioconductor-package
2.05 score 139 dependenciesGMRP - 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
bioconductor-package
0.91 score 20 dependenciesicetea - 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
bioconductor-package
0.82 score 107 dependenciesgwasurvivr - 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
bioconductor-package
1.08 score 133 dependenciesonlineFDR - 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
bioconductor-package
1.00 score 13 dependenciesUlarcirc - 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
bioconductor-package
0.91 score 151 dependenciesslingshot - 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
bioconductor-package
1.80 score 41 dependencies 4 dependentsFastqCleaner - 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
bioconductor-package
0.82 score 91 dependenciesiasva - 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
bioconductor-package
0.82 score 39 dependenciesmaser - 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
bioconductor-package
0.71 score 154 dependenciessigFeature - 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
bioconductor-package
1.64 score 68 dependenciesBiocVersion - Set the appropriate version of Bioconductor packages
This package provides repository information for the appropriate version of Bioconductor.
Last updated 2 months ago
bioconductor-package
6.25 score 0 dependencies 103 dependentsMBttest - 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
bioconductor-package
1.00 score 5 dependenciesnetSmooth - 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
bioconductor-package
1.00 score 168 dependenciesCAGEfightR - 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
bioconductor-package
2.14 score 154 dependencies 1 dependentsMSstatsQCgui - 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
bioconductor-package
0.82 score 140 dependenciessingscore - 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
bioconductor-package
1.45 score 119 dependencies 2 dependentsRandomWalkRestartMH -
Last updated 2 months ago
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 2 months ago
bioconductor-package
2.60 score 96 dependencies 8 dependentsccfindR - 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
bioconductor-package
0.71 score 41 dependenciesigvR - igvR: integrative genomics viewer
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Last updated 2 months ago
bioconductor-package
1.00 score 77 dependencieshipathia - 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
bioconductor-package
1.00 score 150 dependenciesSDAMS - 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
bioconductor-package
0.91 score 60 dependenciesRSeqAn - R SeqAn
Headers and some wrapper functions from the SeqAn C++ library for ease of usage in R.
Last updated 2 months ago
bioconductor-package
0.91 score 1 dependencies 1 dependentsCytoDx - 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
bioconductor-package
0.82 score 39 dependenciesInTAD - 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
bioconductor-package
0.82 score 113 dependenciesTFutils - 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 2 months ago
bioconductor-package
0.91 score 107 dependenciesdecontam - 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
bioconductor-package
2.31 score 33 dependencies 7 dependentsmissRows - 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
bioconductor-package
0.91 score 66 dependenciesrWikiPathways - 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
bioconductor-package
1.75 score 45 dependencies 3 dependentsdiffcyt - 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
bioconductor-package
1.80 score 144 dependencies 4 dependentsplyranges - 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
bioconductor-package
3.38 score 64 dependencies 19 dependentsGateFinder - 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
bioconductor-package
0.91 score 32 dependenciesIMMAN - 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
bioconductor-package
0.82 score 63 dependenciesGSEABenchmarkeR - 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
bioconductor-package
1.45 score 103 dependenciesSconify - 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
bioconductor-package
0.71 score 54 dependenciesphantasus - 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
bioconductor-package
2.18 score 142 dependenciesiCNV - Integrated Copy Number Variation detection
Integrative copy number variation (CNV) detection from multiple platform and experimental design.
Last updated 2 months ago
bioconductor-package
0.82 score 91 dependenciesSummarizedBenchmark - Classes and methods for performing benchmark comparisons
This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the results of applying different methods to a shared data set. This class provides an integrated interface to store metadata such as method parameters and software versions as well as ground truths (when these are available) and evaluation metrics.
Last updated 2 months ago
bioconductor-package
1.58 score 76 dependenciesFELLA - 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
bioconductor-package
0.71 score 33 dependenciesdiffcoexp - 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
bioconductor-package
1.31 score 118 dependencies 1 dependentsDEScan2 - Differential Enrichment Scan 2
Integrated peak and differential caller, specifically designed for broad epigenomic signals.
Last updated 2 months ago
bioconductor-package
1.08 score 125 dependenciesMDTS - 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
bioconductor-package
1.45 score 51 dependenciesGeneStructureTools - 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
bioconductor-package
0.61 score 150 dependenciestRNAscanImport - 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
bioconductor-package
0.82 score 80 dependenciesvidger - 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
bioconductor-package
0.91 score 115 dependenciesdmrseq - 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
bioconductor-package
1.38 score 138 dependencies 1 dependentsddPCRclust - 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
bioconductor-package
0.71 score 93 dependenciesmartini - 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
bioconductor-package
0.82 score 20 dependenciesDominoEffect - 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
bioconductor-package
1.08 score 96 dependenciesscmeth - 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
bioconductor-package
1.00 score 152 dependenciesenrichplot - 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 2 months ago
bioconductor-package
5.17 score 115 dependencies 54 dependentskissDE - 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
bioconductor-package
1.24 score 187 dependenciespowerTCR - 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
bioconductor-package
0.82 score 27 dependenciesTTMap - 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
bioconductor-package
0.61 score 55 dependenciesomicplotR - 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
bioconductor-package
0.61 score 105 dependenciesBEARscc - 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 2 months ago
bioconductor-package
0.91 score 55 dependenciessrnadiff - 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 2 months ago
bioconductor-package
1.08 score 202 dependenciesTrendy - 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
bioconductor-package
0.82 score 89 dependenciespogos - 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
bioconductor-package
0.71 score 123 dependenciesmCSEA - 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 2 months ago
bioconductor-package
1.64 score 162 dependenciesDropletUtils - 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 2 months ago
bioconductor-package
3.66 score 56 dependencies 7 dependentshmdbQuery - 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
bioconductor-package
0.71 score 3 dependenciesdrawProteins - 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
bioconductor-package
1.16 score 53 dependencies 1 dependentsscFeatureFilter - 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
bioconductor-package
0.82 score 31 dependenciesTFEA.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
bioconductor-package
0.71 score 96 dependenciesMetaNeighbor - Single cell replicability analysis
MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.
Last updated 2 months ago
bioconductor-package
1.08 score 69 dependenciesomicsPrint - 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
bioconductor-package
0.82 score 52 dependenciesloci2path - 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
bioconductor-package
1.31 score 42 dependenciesOmaDB - R wrapper for the OMA REST API
A package for the orthology prediction data download from OMA database.
Last updated 2 months ago
bioconductor-package
1.08 score 50 dependenciesbcSeq - 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
bioconductor-package
0.61 score 21 dependenciesgep2pep - 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
bioconductor-package
0.61 score 51 dependenciestranscriptogramer - 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
bioconductor-package
0.71 score 92 dependenciesrunibic - 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
bioconductor-package
0.82 score 83 dependenciestenXplore -
Last updated 2 months ago
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
bioconductor-package
0.82 score 41 dependenciesMetaCyto - 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
bioconductor-package
0.91 score 108 dependenciesPROPS - 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 2 months ago
bioconductor-package
0.61 score 69 dependenciesoncomix - 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
bioconductor-package
0.82 score 56 dependenciesSeqSQC - 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
bioconductor-package
1.24 score 121 dependenciesivygapSE - 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
bioconductor-package
0.82 score 148 dependenciesontoProc - 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 2 months ago
bioconductor-package
1.45 score 108 dependencies 1 dependentsstageR - 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
bioconductor-package
1.00 score 28 dependenciestopdownr - 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
bioconductor-package
1.00 score 128 dependenciesprogeny - 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
bioconductor-package
1.64 score 55 dependencies 1 dependentsscPipe - 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 2 months ago
bioconductor-package
1.64 score 173 dependenciesbnbc - Bandwise normalization and batch correction of Hi-C data
Tools to normalize (several) Hi-C data from replicates.
Last updated 2 months ago
bioconductor-package
1.24 score 132 dependenciesANF - 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
bioconductor-package
0.91 score 16 dependenciesmethimpute - 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
bioconductor-package
1.00 score 53 dependencieschromVAR - 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
bioconductor-package
1.24 score 152 dependencies 1 dependentsomicRexposome - 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
bioconductor-package
1.24 score 216 dependenciesMIRA - 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
bioconductor-package
1.16 score 93 dependencies 1 dependentsvulcan - 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
bioconductor-package
0.82 score 191 dependenciesMSstatsQC - 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
bioconductor-package
1.31 score 138 dependencies 1 dependentspanelcn.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
bioconductor-package
0.91 score 33 dependenciesseqCAT - 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
bioconductor-package
0.82 score 96 dependenciesmultiMiR - 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
bioconductor-package
0.91 score 51 dependenciesAUCell - 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
bioconductor-package
1 stars 1.90 score 112 dependencies 4 dependentsopenPrimeR - 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
bioconductor-package
0.91 score 106 dependenciesamplican - 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
bioconductor-package
1.24 score 118 dependenciesTFARM - 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
bioconductor-package
0.91 score 40 dependenciesChIPanalyser - 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
bioconductor-package
0.82 score 59 dependenciesRbowtie2 - 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
bioconductor-package
1.75 score 32 dependencies 3 dependentsseqcombo - Visualization Tool for Genetic Reassortment
Provides useful functions for visualizing virus reassortment events.
Last updated 2 months ago
bioconductor-package
0.82 score 36 dependenciesSPONGE - 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
bioconductor-package
1.16 score 217 dependencies 1 dependentsmicrobiome - Microbiome Analytics
Utilities for microbiome analysis.
Last updated 2 months ago
bioconductor-package
1.95 score 84 dependencies 3 dependentsDoscheda - 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
bioconductor-package
0.91 score 150 dependenciesTMixClust - 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
bioconductor-package
0.71 score 23 dependenciescytolib - 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
bioconductor-package
5.14 score 3 dependencies 57 dependentsM3C - 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
bioconductor-package
1.00 score 52 dependencies 1 dependentszFPKM - 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
bioconductor-package
0.71 score 63 dependenciesCEMiTool - 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
bioconductor-package
1.38 score 186 dependenciesRVS - 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
bioconductor-package
0.91 score 52 dependenciesrexposome - 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
bioconductor-package
1.31 score 156 dependencies 1 dependentsGENIE3 - 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
bioconductor-package
6.30 score 21 dependencies 4 dependentsSCnorm - 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
bioconductor-package
3.06 score 71 dependenciesepivizrChart - 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
bioconductor-package
0.91 score 109 dependenciesdiffuStats - 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
bioconductor-package
0.71 score 41 dependenciesconsensusOV - 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
bioconductor-package
1.31 score 143 dependencies 1 dependentsClusterJudge - 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
bioconductor-package
0.82 score 19 dependenciesOPWeight - 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
bioconductor-package
0.82 score 34 dependenciesphenopath - 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
bioconductor-package
1 stars 0.91 score 62 dependenciesscmap - 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
bioconductor-package
0.82 score 68 dependenciesscoreInvHap - 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
bioconductor-package
0.91 score 72 dependenciesRhdf5lib - hdf5 library as an R package
Provides C and C++ hdf5 libraries.
Last updated 2 months ago
bioconductor-package
8.94 score 0 dependencies 321 dependentsRProtoBufLib - 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
bioconductor-package
5.15 score 0 dependencies 58 dependentsmfa - 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
bioconductor-package
1.08 score 73 dependencieszinbwave - 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
bioconductor-package
2.31 score 68 dependencies 7 dependentsScale4C - 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
bioconductor-package
0.61 score 29 dependenciesIsoformSwitchAnalyzeR - 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
bioconductor-package
1.16 score 145 dependenciesmotifmatchr - 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
bioconductor-package
1.95 score 117 dependencies 6 dependentsmiRBaseConverter - 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
bioconductor-package
1.24 score 0 dependencies 2 dependentsmethInheritSim - 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
bioconductor-package
0.82 score 100 dependenciesndexr - 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
bioconductor-package
1.08 score 34 dependenciesGA4GHshiny - 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
bioconductor-package
0.82 score 115 dependenciesmsgbsR -
Last updated 2 months ago
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
bioconductor-package
0.91 score 134 dependenciesheatmaps - 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
bioconductor-package
0.91 score 57 dependencies 1 dependentsideal - 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.
Last updated 2 months ago
bioconductor-package
1.31 score 201 dependenciescellbaseR - 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
bioconductor-package
1.64 score 58 dependenciesBLMA - 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
bioconductor-package
0.91 score 68 dependenciesmethylInheritance - 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
bioconductor-package
0.82 score 103 dependenciessemisup - 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
bioconductor-package
0.82 score 1 dependenciesIMAS - Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative splicing.
Last updated 2 months ago
bioconductor-package
2.14 score 107 dependenciesGenomicScores - 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
bioconductor-package
2.42 score 73 dependencies 6 dependentsRaggedExperiment - 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 2 months ago
bioconductor-package
2.92 score 29 dependencies 13 dependentsbanocc - 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
bioconductor-package
0.91 score 56 dependenciesAnnotationFilter - 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
bioconductor-package
7.17 score 18 dependencies 154 dependentswiggleplotr - 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
bioconductor-package
1.24 score 80 dependencies 1 dependentsGA4GHclient - 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
bioconductor-package
1.00 score 79 dependencies 1 dependentscydar - 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
bioconductor-package
0.82 score 91 dependenciesBiocFileCache - 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
bioconductor-package
9.60 score 39 dependencies 411 dependentsBioCor - 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
bioconductor-package
1.16 score 53 dependenciesbranchpointer - 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
bioconductor-package
0.61 score 147 dependenciesIntEREst - Intron-Exon Retention Estimator
This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).
Last updated 2 months ago
bioconductor-package
0.91 score 130 dependenciesrqt - 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
bioconductor-package
1.00 score 144 dependenciesOrganism.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
bioconductor-package
1.38 score 86 dependencies 1 dependentsswfdr - 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
bioconductor-package
1.31 score 0 dependenciesREMP - 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
bioconductor-package
1.00 score 186 dependenciesgeneClassifiers - 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
bioconductor-package
0.71 score 2 dependenciesRTNduals - 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
bioconductor-package
1.00 score 135 dependencies 1 dependentsMCbiclust - 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
bioconductor-package
0.91 score 133 dependenciesdiscordant - 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
bioconductor-package
1.16 score 24 dependencieskaryoploteR - 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
bioconductor-package
1.80 score 130 dependencies 4 dependentsChIPexoQual - ChIPexoQual
Package with a quality control pipeline for ChIP-exo/nexus data.
Last updated 2 months ago
bioconductor-package
0.91 score 133 dependenciesfuntooNorm - 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
bioconductor-package
1.38 score 133 dependenciesmimager - mimager: The Microarray Imager
Easily visualize and inspect microarrays for spatial artifacts.
Last updated 2 months ago
bioconductor-package
0.91 score 66 dependenciescoseq - 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
bioconductor-package
2.00 score 85 dependenciesTCseq - 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
bioconductor-package
1.08 score 80 dependenciesRJMCMCNucleosomes - 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
bioconductor-package
0.61 score 59 dependenciestreeio - 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
bioconductor-package
6.53 score 34 dependencies 111 dependentsscone - 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
bioconductor-package
1.45 score 176 dependenciesscDD - 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
bioconductor-package
0.91 score 121 dependenciesclusterSeq - 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
bioconductor-package
1.08 score 34 dependenciesgcapc - 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
bioconductor-package
0.82 score 51 dependencieschimeraviz - Visualization tools for gene fusions
chimeraviz manages data from fusion gene finders and provides useful visualization tools.
Last updated 2 months ago
bioconductor-package
1.00 score 163 dependenciesIWTomics - 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
bioconductor-package
0.91 score 64 dependenciesMWASTools - 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
bioconductor-package
1.08 score 112 dependencies 1 dependentsphosphonormalizer - 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
bioconductor-package
0.82 score 3 dependenciesBPRMeth - 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
bioconductor-package
1.16 score 87 dependencies 1 dependentsyarn - 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
bioconductor-package
1.08 score 154 dependencies 1 dependentsCCPROMISE - 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
bioconductor-package
0.61 score 45 dependenciesyamss - 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
bioconductor-package
1.00 score 68 dependenciesregsplice - 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
bioconductor-package
1.00 score 41 dependenciesM3Drop - 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
bioconductor-package
1.64 score 160 dependencies 2 dependentsannotatr - 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
bioconductor-package
1.75 score 113 dependencies 4 dependentsHelloRanges - 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
bioconductor-package
1.00 score 71 dependencies 1 dependentsPathoStat - 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
bioconductor-package
1.31 score 198 dependenciesMAST - Model-based Analysis of Single Cell Transcriptomics
Methods and models for handling zero-inflated single cell assay data.
Last updated 2 months ago
bioconductor-package
2.09 score 63 dependencies 5 dependentsflowPloidy - 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
bioconductor-package
0.91 score 100 dependenciesKEGGlincs - 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
bioconductor-package
0.82 score 55 dependenciesGOpro - 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
bioconductor-package
0.82 score 87 dependenciesSPLINTER - 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
bioconductor-package
0.91 score 152 dependenciesFitHiC - 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
bioconductor-package
0.82 score 3 dependenciesPi -
Last updated 2 months ago
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
bioconductor-package
0.71 score 85 dependenciesBaalChIP - 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
bioconductor-package
0.71 score 111 dependenciesBiocWorkflowTools - 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
bioconductor-package
1.00 score 55 dependenciessigneR - 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
bioconductor-package
1.16 score 232 dependenciesMetaboSignal - 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
bioconductor-package
1.08 score 188 dependenciesphilr - 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
bioconductor-package
1.08 score 58 dependenciesgeneAttribution - 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
bioconductor-package
0.61 score 69 dependenciesAnaquin - 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
bioconductor-package
0.82 score 82 dependenciesPharmacoGx - 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
bioconductor-package
2.27 score 145 dependencies 3 dependentsGAprediction - Prediction of gestational age with Illumina HumanMethylation450 data
[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data.
Last updated 2 months ago
bioconductor-package
0.71 score 10 dependenciesGRmetrics - Calculate growth-rate inhibition (GR) metrics
Functions for calculating and visualizing growth-rate inhibition (GR) metrics.
Last updated 2 months ago
bioconductor-package
0.91 score 113 dependenciesswitchde - 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
bioconductor-package
0.91 score 57 dependenciesCellMapper - 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
bioconductor-package
1 stars 0.91 score 2 dependenciesBayesKnockdown - 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
bioconductor-package
0.61 score 2 dependenciesASpli - Analysis of Alternative Splicing Using RNA-Seq
Integrative pipeline for the analysis of alternative splicing using RNAseq.
Last updated 2 months ago
bioconductor-package
2.18 score 164 dependencies 1 dependentsctsGE - 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
bioconductor-package
1.00 score 63 dependenciesMODA - 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
bioconductor-package
0.61 score 106 dependenciesSNPediaR - 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
bioconductor-package
0.82 score 3 dependenciesGeneGeneInteR - 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
bioconductor-package
0.71 score 137 dependenciesASAFE - 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
bioconductor-package
0.61 score 0 dependenciesmaftools - 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
bioconductor-package
3.72 score 8 dependencies 18 dependentsmethylKit - 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 2 months ago
bioconductor-package
1.95 score 96 dependencies 3 dependentsAMOUNTAIN - 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
bioconductor-package
0.91 score 0 dependencies 1 dependentsclusterExperiment - 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
bioconductor-package
2.53 score 137 dependencies 1 dependentsMGFR - Marker Gene Finder in RNA-seq data
The package is designed to detect marker genes from RNA-seq data.
Last updated 2 months ago
bioconductor-package
1.08 score 65 dependencies 1 dependentsCytoML - 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
bioconductor-package
1.45 score 75 dependenciesfgsea - 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 months ago
bioconductor-package
6.20 score 41 dependencies 97 dependentsqsea - 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
bioconductor-package
0.91 score 56 dependenciesccmap - 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
bioconductor-package
0.91 score 50 dependenciesnormr - 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
bioconductor-package
1.00 score 81 dependencieschromstaR - 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 2 months ago
bioconductor-package
1.08 score 78 dependenciesesetVis - 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
bioconductor-package
1.00 score 50 dependenciesMetCirc - 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
bioconductor-package
1.64 score 73 dependenciescrossmeta - 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 2 months ago
bioconductor-package
0.91 score 147 dependenciessights - 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
bioconductor-package
0.91 score 34 dependenciesgeneplast - 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
bioconductor-package
0.82 score 17 dependenciescovEB - 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
bioconductor-package
0.82 score 16 dependenciesMADSEQ - 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
bioconductor-package
0.82 score 99 dependenciesGEM - 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
bioconductor-package
0.82 score 28 dependenciesnetprioR - 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
bioconductor-package
0.71 score 40 dependenciesbioCancer - 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
bioconductor-package
1.24 score 245 dependenciescovRNA - 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
bioconductor-package
0.71 score 53 dependenciesepivizrStandalone - 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
bioconductor-package
0.91 score 117 dependenciesEGAD - 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
bioconductor-package
1.16 score 57 dependenciesMMDiff2 - 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
bioconductor-package
0.71 score 96 dependenciesEGSEA - 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
bioconductor-package
1.24 score 189 dependenciesCHRONOS - 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
bioconductor-package
0.82 score 83 dependenciesepivizrData - Data Management API for epiviz interactive visualization app
Serve data from Bioconductor Objects through a WebSocket connection.
Last updated 2 months ago
bioconductor-package
1.75 score 106 dependencies 4 dependentsepivizrServer - 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
bioconductor-package
2.00 score 10 dependencies 5 dependentsHarman - 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
bioconductor-package
2.67 score 5 dependencies 1 dependentsMultiDataSet - 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
bioconductor-package
2.70 score 59 dependencies 11 dependentsPureCN - 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
bioconductor-package
1.95 score 97 dependenciesInteractionSet - 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
bioconductor-package
4.17 score 29 dependencies 34 dependentsLymphoSeq - 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
bioconductor-package
0.82 score 91 dependenciesBgeeDB - 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
bioconductor-package
2.31 score 64 dependencies 2 dependentspqsfinder - 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
bioconductor-package
0.82 score 21 dependenciesoppar - 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
bioconductor-package
0.91 score 94 dependenciespcaExplorer - 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 months ago
bioconductor-package
1.38 score 177 dependencies 1 dependentsscran - 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
bioconductor-package
4.28 score 66 dependencies 34 dependentsGlimma - 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
bioconductor-package
3.36 score 89 dependencies 2 dependentsodseq - 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
bioconductor-package
1.00 score 31 dependencies 1 dependentsCONFESS - Cell OrderiNg by FluorEScence Signal
Single Cell Fluidigm Spot Detector.
Last updated 2 months ago
bioconductor-package
0.91 score 141 dependenciesLinnorm - 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
bioconductor-package
1.95 score 58 dependencies 5 dependentsBadRegionFinder - 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
bioconductor-package
0.82 score 94 dependenciesEBSEA - 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
bioconductor-package
0.82 score 67 dependenciesCINdex - 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
bioconductor-package
1.00 score 43 dependenciesDEFormats - Differential gene expression data formats converter
Convert between different data formats used by differential gene expression analysis tools.
Last updated 2 months ago
bioconductor-package
1.24 score 72 dependencies 1 dependentsrecoup - 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
bioconductor-package
1.16 score 116 dependenciesAneuFinder - 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
bioconductor-package
3.14 score 83 dependenciesOncoScore - 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
bioconductor-package
2.27 score 62 dependenciesISoLDE - 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
bioconductor-package
0.82 score 0 dependenciesDRIMSeq - 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
bioconductor-package
3.36 score 62 dependencies 2 dependentsDNAshapeR - 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
bioconductor-package
1.08 score 25 dependenciesSwathXtend -
Last updated 2 months ago
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
bioconductor-package
1.16 score 38 dependenciesPCAN - 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
bioconductor-package
0.82 score 9 dependenciesdoppelgangR - 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
bioconductor-package
1.31 score 72 dependenciespsygenet2r - psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Package to retrieve data from PsyGeNET database (www.psygenet.org) and to perform comorbidity studies with PsyGeNET's and user's data.
Last updated 2 months ago
bioconductor-package
1.08 score 93 dependenciesmiRNAmeConverter - 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
bioconductor-package
0.82 score 46 dependenciesnucleoSim - 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
bioconductor-package
1.00 score 3 dependenciesUniquorn - 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
bioconductor-package
1.51 score 81 dependenciesExperimentHubData - Add resources to ExperimentHub
Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.
Last updated 2 months ago
bioconductor-package
1.24 score 116 dependencies 1 dependentsExperimentHub - 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
bioconductor-package
5.17 score 59 dependencies 55 dependentsdada2 - 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
bioconductor-package
2.35 score 82 dependencies 4 dependentscellity - 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
bioconductor-package
0.91 score 73 dependencieschromPlot - 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
bioconductor-package
0.82 score 63 dependenciesRImmPort - 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
bioconductor-package
0.91 score 36 dependenciesExpressionAtlas - 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
bioconductor-package
0.91 score 60 dependenciesmetaCCA - 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
bioconductor-package
0.82 score 0 dependenciesMergeomics - 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
bioconductor-package
0.82 score 0 dependenciesSMITE - 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
bioconductor-package
2.22 score 145 dependenciestximport - 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
bioconductor-package
2.76 score 0 dependencies 10 dependentsBasicSTARRseq - 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
bioconductor-package
0.82 score 42 dependenciesROTS - Reproducibility-Optimized Test Statistic
Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.
Last updated 2 months ago
bioconductor-package
1.45 score 3 dependencies 2 dependentsRGraph2js - 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
bioconductor-package
0.71 score 5 dependenciesIHW - 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
bioconductor-package
1.45 score 4 dependencies 2 dependentsGenVisR - Genomic Visualizations in R
Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.
Last updated 2 months ago
bioconductor-package
1.69 score 114 dependenciesflowAI - 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
bioconductor-package
1.64 score 66 dependencies 3 dependentsEmpiricalBrownsMethod - 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
bioconductor-package
1.45 score 0 dependencies 3 dependentsSC3 - Single-Cell Consensus Clustering
A tool for unsupervised clustering and analysis of single cell RNA-Seq data.
Last updated 2 months ago
bioconductor-package
1.45 score 98 dependencies 1 dependentsggcyto - 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
bioconductor-package
2.18 score 61 dependencies 5 dependentsGSALightning - 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
bioconductor-package
0.82 score 3 dependenciesCrispRVariants - 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
bioconductor-package
3.26 score 85 dependenciessplineTimeR - 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
bioconductor-package
0.82 score 55 dependencieslpsymphony - 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
bioconductor-package
1.58 score 0 dependencies 3 dependentsprofileScoreDist - Profile score distributions
Regularization and score distributions for position count matrices.
Last updated 2 months ago
bioconductor-package
0.71 score 2 dependenciesdcGSA - 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
bioconductor-package
0.91 score 11 dependenciesbiomformat - 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
bioconductor-package
4.32 score 8 dependencies 36 dependentsBioQC - 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
bioconductor-package
1.16 score 8 dependenciesFamAgg - 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
bioconductor-package
0.91 score 85 dependenciesiCOBRA - 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
bioconductor-package
1.31 score 82 dependencies 1 dependentsChicago - CHiCAGO: Capture Hi-C Analysis of Genomic Organization
A pipeline for analysing Capture Hi-C data.
Last updated 2 months ago
bioconductor-package
1.00 score 67 dependenciesconsensusSeekeR - 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
bioconductor-package
1.16 score 57 dependencies 1 dependentsglobalSeq - 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
bioconductor-package
1.08 score 0 dependenciesR4RNA - 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
bioconductor-package
1.64 score 18 dependencies 4 dependentssubSeq - 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
bioconductor-package
1.00 score 44 dependenciesbiobroom - 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
bioconductor-package
1.16 score 25 dependencies 1 dependentsmiRcomp - 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
bioconductor-package
1.00 score 4 dependenciesRCy3 - 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
bioconductor-package
3.60 score 42 dependencies 15 dependentsRiboProfiling - 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
bioconductor-package
0.82 score 165 dependenciesGeneBreak - Gene Break Detection
Recurrent breakpoint gene detection on copy number aberration profiles.
Last updated 2 months ago
bioconductor-package
0.82 score 51 dependenciesGUIDEseq - 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
bioconductor-package
1.16 score 171 dependenciesSWATH2stats - 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
bioconductor-package
2.42 score 81 dependenciesSICtools - 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
bioconductor-package
0.71 score 45 dependenciesProstar - 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
bioconductor-package
1.51 score 179 dependenciesMEAL - 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
bioconductor-package
2.80 score 216 dependenciesiCheck - 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
bioconductor-package
1.85 score 175 dependenciesDAPAR - 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
bioconductor-package
1.69 score 140 dependencies 1 dependentsGuitar - 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
bioconductor-package
0.91 score 94 dependenciesEnrichedHeatmap - 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
bioconductor-package
2.92 score 38 dependencies 1 dependentsdupRadar - Assessment of duplication rates in RNA-Seq datasets
Duplication rate quality control for RNA-Seq datasets.
Last updated 2 months ago
bioconductor-package
1.00 score 4 dependenciesDiffLogo - DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo is an easy-to-use tool to visualize motif differences.
Last updated 2 months ago
bioconductor-package
0.82 score 2 dependenciesRTCGA - 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
bioconductor-package
1.24 score 118 dependencies 1 dependentsLOLA - 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
bioconductor-package
1.00 score 29 dependenciesiGC - 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
bioconductor-package
0.82 score 3 dependenciesAnnotationHubData - 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
bioconductor-package
2.09 score 114 dependencies 3 dependentssevenbridges - 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
bioconductor-package
1.00 score 24 dependenciesldblock - data structures for linkage disequilibrium measures in populations
Define data structures for linkage disequilibrium measures in populations.
Last updated 2 months ago
bioconductor-package
0.91 score 12 dependenciesPath2PPI - 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
bioconductor-package
0.71 score 11 dependenciesmyvariant - 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
bioconductor-package
0.91 score 122 dependenciesChIPComp - 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
bioconductor-package
0.71 score 54 dependenciesBBCAnalyzer - 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
bioconductor-package
1.16 score 70 dependenciesTCGAbiolinks - 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
bioconductor-package
2.76 score 105 dependencies 6 dependentssynlet - 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
bioconductor-package
0.82 score 33 dependenciesNanoStringDiff - 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
bioconductor-package
0.82 score 4 dependencieseudysbiome - 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
bioconductor-package
0.71 score 36 dependenciesOscope - 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
bioconductor-package
1.24 score 52 dependencies 1 dependentsHilbertCurve - 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
bioconductor-package
1.00 score 26 dependenciesLedPred - 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
bioconductor-package
0.91 score 64 dependenciestraseR - 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
bioconductor-package
0.82 score 51 dependenciesmiRLAB - 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
bioconductor-package
1.00 score 187 dependenciesDeMAND - 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
bioconductor-package
1.00 score 1 dependenciesrnaseqcomp - 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
bioconductor-package
0.91 score 1 dependenciesINSPEcT - 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
bioconductor-package
1.16 score 120 dependenciesCNVPanelizer - 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
bioconductor-package
1.24 score 108 dependenciesfCI - 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
bioconductor-package
1.00 score 42 dependenciesIONiseR - 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
bioconductor-package
0.91 score 89 dependencieserma -
Last updated 2 months ago
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
bioconductor-package
0.91 score 68 dependencieshierGWAS - 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
bioconductor-package
0.82 score 12 dependenciesELMER - 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
bioconductor-package
3.49 score 203 dependenciesCausalR - Causal network analysis methods
Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.
Last updated 2 months ago
bioconductor-package
1.00 score 11 dependenciesBEclear - 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
bioconductor-package
1.58 score 22 dependenciesedge - 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
bioconductor-package
1.16 score 85 dependenciessimilaRpeak - 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
bioconductor-package
1.00 score 1 dependenciesmsa - 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
bioconductor-package
2.42 score 19 dependencies 6 dependentsR3CPET - 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
bioconductor-package
1.45 score 165 dependenciespandaR - PANDA Algorithm
Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.
Last updated 2 months ago
bioconductor-package
1.51 score 38 dependencies 1 dependentsMethTargetedNGS - Perform Methylation Analysis on Next Generation Sequencing Data
Perform step by step methylation analysis of Next Generation Sequencing data.
Last updated 2 months ago
bioconductor-package
1 stars 1.24 score 42 dependenciesconumee - 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
bioconductor-package
0.82 score 135 dependenciesTPP - 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
bioconductor-package
5.13 score 86 dependenciesRUVcorr - 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
bioconductor-package
0.91 score 32 dependenciesmogsa - 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
bioconductor-package
0.91 score 61 dependenciesFISHalyseR - 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
bioconductor-package
0.82 score 38 dependenciesDMRcaller - 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
bioconductor-package
2.09 score 28 dependenciesregioneR - 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
bioconductor-package
3.40 score 54 dependencies 20 dependentspmm - 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
bioconductor-package
0.82 score 10 dependenciesComplexHeatmap - 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
bioconductor-package
8.18 score 20 dependencies 135 dependentsRBM - 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
bioconductor-package
2.94 score 3 dependenciespodkat - 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
bioconductor-package
1.08 score 51 dependenciesgtrellis - 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
bioconductor-package
1.31 score 24 dependencies 1 dependentsTIN - 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
bioconductor-package
2.70 score 124 dependenciesInPAS - 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 months ago
bioconductor-package
1.00 score 137 dependenciesbamsignals - 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
bioconductor-package
2.83 score 19 dependencies 12 dependentsSIMAT - 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
bioconductor-package
0.91 score 39 dependenciesMatrixRider - 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
bioconductor-package
1.00 score 116 dependenciesdiggit - Inference of Genetic Variants Driving Cellular Phenotypes
Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm
Last updated 2 months ago
bioconductor-package
1.08 score 87 dependenciescanceR - 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
bioconductor-package
1.16 score 203 dependenciesmuscle - Multiple Sequence Alignment with MUSCLE
MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.
Last updated 2 months ago
bioconductor-package
0.82 score 18 dependenciesBrowserViz - 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
bioconductor-package
1.58 score 10 dependencies 2 dependentssigsquared - 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
bioconductor-package
0.91 score 5 dependenciesSELEX - Functions for analyzing SELEX-seq data
Tools for quantifying DNA binding specificities based on SELEX-seq data.
Last updated 2 months ago
bioconductor-package
5.76 score 19 dependenciesProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
Last updated 2 months ago
bioconductor-package
7.46 score 0 dependencies 175 dependentsBubbleTree - 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
bioconductor-package
0.82 score 141 dependenciesrGREAT - 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
bioconductor-package
2.00 score 113 dependencies 2 dependentsGreyListChIP - 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
bioconductor-package
1.85 score 51 dependencies 4 dependentsIVAS - Identification of genetic Variants affecting Alternative Splicing
Identification of genetic variants affecting alternative splicing.
Last updated 2 months ago
bioconductor-package
1.16 score 121 dependencies 1 dependentsggtree - 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
bioconductor-package
6.33 score 53 dependencies 96 dependentsparglms - 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
bioconductor-package
0.82 score 31 dependenciesseqPattern - 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
bioconductor-package
2.09 score 21 dependencies 7 dependentsgespeR - Gene-Specific Phenotype EstimatoR
Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.
Last updated 2 months ago
bioconductor-package
0.91 score 110 dependenciesCODEX - 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
bioconductor-package
1.16 score 51 dependencies 1 dependentschromDraw - 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
bioconductor-package
0.71 score 18 dependenciesrgsepd - 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
bioconductor-package
1.16 score 119 dependenciesFlowSOM - 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
bioconductor-package
2.46 score 88 dependencies 9 dependentsPROPER - 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
bioconductor-package
3.78 score 6 dependencies 1 dependentscpvSNP - 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
bioconductor-package
0.82 score 94 dependenciesQuartPAC - 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
bioconductor-package
1.08 score 47 dependenciesgenomation - 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
bioconductor-package
2.31 score 96 dependencies 5 dependentsAIMS - 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
bioconductor-package
1.69 score 6 dependencies 4 dependentspepXMLTab - 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
bioconductor-package
0.82 score 1 dependenciesseqTools - 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
bioconductor-package
1.00 score 1 dependencies 1 dependentsmygene - 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
bioconductor-package
1.45 score 139 dependencies 1 dependentsspecL - 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
bioconductor-package
0.91 score 27 dependenciesCOSNet - 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
bioconductor-package
0.82 score 0 dependenciesCFAssay - 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
bioconductor-package
2.00 score 0 dependenciesRqc - 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
bioconductor-package
0.91 score 149 dependenciesMBAmethyl - 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
bioconductor-package
0.71 score 0 dependenciesBridgeDbR - 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
bioconductor-package
1.31 score 2 dependenciestracktables - 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
bioconductor-package
0.82 score 47 dependenciesIMPCdata - Retrieves data from IMPC database
Package contains methods for data retrieval from IMPC Database.
Last updated 2 months ago
bioconductor-package
0.82 score 1 dependenciesgroHMM - GRO-seq Analysis Pipeline
A pipeline for the analysis of GRO-seq data.
Last updated 2 months ago
bioconductor-package
1.16 score 50 dependenciesSGSeq - 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
bioconductor-package
1.51 score 71 dependencies 3 dependentsSTATegRa - Classes and methods for multi-omics data integration
Classes and tools for multi-omics data integration.
Last updated 2 months ago
bioconductor-package
1.31 score 50 dependenciescsaw - 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 2 months ago
bioconductor-package
2.18 score 47 dependencies 7 dependentsflowCHIC - 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
bioconductor-package
0.91 score 74 dependenciesMAIT - 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
bioconductor-package
1.00 score 195 dependenciesGenomicTuples - 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 2 months ago
bioconductor-package
1.00 score 19 dependenciespaxtoolsr - 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 2 months ago
bioconductor-package
1.58 score 44 dependenciesASGSCA - 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
bioconductor-package
0.71 score 3 dependenciesproBAMr - 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
bioconductor-package
1.00 score 93 dependenciesIdeoViz - Plots data (continuous/discrete) along chromosomal ideogram
Plots data associated with arbitrary genomic intervals along chromosomal ideogram.
Last updated 2 months ago
bioconductor-package
0.91 score 50 dependenciesregionReport - 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 2 months ago
bioconductor-package
0.82 score 151 dependenciesderfinderHelper - 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 2 months ago
bioconductor-package
2.27 score 5 dependencies 8 dependentsderfinderPlot - 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 2 months ago
bioconductor-package
1.08 score 173 dependencies 1 dependentsderfinder - 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 2 months ago
bioconductor-package
2.35 score 134 dependencies 7 dependentspolyester - Simulate RNA-seq reads
This package can be used to simulate RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.
Last updated 2 months ago
bioconductor-package
1.64 score 21 dependenciesGenomicInteractions - 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
bioconductor-package
2.09 score 149 dependencies 6 dependentsrRDP - 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
bioconductor-package
1.24 score 19 dependenciesMGFM - 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
bioconductor-package
1.08 score 41 dependencies 1 dependentsMSnID - 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
bioconductor-package
1.08 score 160 dependenciesTSCAN - 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
bioconductor-package
4.93 score 86 dependencies 3 dependentsrain - 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
bioconductor-package
0.82 score 8 dependenciesswitchBox - 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
bioconductor-package
1.16 score 8 dependencies 1 dependentsRnits - 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
bioconductor-package
0.91 score 45 dependenciesmethylPipe - 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
bioconductor-package
1.24 score 154 dependencies 1 dependentsMBASED - 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
bioconductor-package
0.71 score 38 dependencieshiReadsProcessor - 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
bioconductor-package
0.91 score 89 dependencieserccdashboard - 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
bioconductor-package
1.08 score 45 dependenciescompEpiTools - 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
bioconductor-package
1.00 score 159 dependenciesquantro - 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
bioconductor-package
1.38 score 141 dependencies 2 dependentsSemDist - 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
bioconductor-package
0.91 score 42 dependenciesRUVnormalize - 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
bioconductor-package
0.71 score 3 dependenciesMPFE - 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
bioconductor-package
0.91 score 0 dependenciesmiRNAtap - 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
bioconductor-package
1.00 score 47 dependenciesmetabomxtr - 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
bioconductor-package
0.91 score 48 dependenciesinteractiveDisplayBase - 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
bioconductor-package
1.31 score 42 dependencies 1 dependentsballgown - 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
bioconductor-package
1.64 score 80 dependencies 1 dependentsMultiMed - Testing multiple biological mediators simultaneously
Implements methods for testing multiple mediators
Last updated 2 months ago
bioconductor-package
0.71 score 0 dependenciesGSReg - 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
bioconductor-package
0.82 score 101 dependenciesshinyMethyl - 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
bioconductor-package
1.08 score 144 dependenciesPviz - Peptide Annotation and Data Visualization using Gviz
Pviz adapts the Gviz package for protein sequences and data.
Last updated 2 months ago
bioconductor-package
0.71 score 147 dependenciespRolocGUI - 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
bioconductor-package
1.31 score 233 dependenciespepStat - Statistical analysis of peptide microarrays
Statistical analysis of peptide microarrays
Last updated 2 months ago
bioconductor-package
0.71 score 54 dependenciesoposSOM - 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
bioconductor-package
0.91 score 78 dependenciesflowDensity - 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
bioconductor-package
3.33 score 82 dependencies 3 dependentsriboSeqR - 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
bioconductor-package
1.08 score 40 dependenciesssviz - A small RNA-seq visualizer and analysis toolkit
Small RNA sequencing viewer
Last updated 2 months ago
bioconductor-package
0.91 score 61 dependenciesRGSEA - 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
bioconductor-package
0.82 score 1 dependenciesRUVSeq - 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
bioconductor-package
1.90 score 113 dependencies 5 dependentsflowClean - flowClean
A quality control tool for flow cytometry data based on compositional data analysis.
Last updated 2 months ago
bioconductor-package
1.00 score 16 dependenciesMethylAid - 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
bioconductor-package
0.82 score 156 dependenciesmonocle - 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
bioconductor-package
5.31 score 68 dependencies 2 dependentsfastLiquidAssociation - 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
bioconductor-package
0.91 score 114 dependenciesmeshr - 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
bioconductor-package
1.16 score 75 dependencies 1 dependentsMeSHDbi - 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
bioconductor-package
1.80 score 38 dependencies 3 dependentsGenomicFiles - 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
bioconductor-package
3.21 score 70 dependencies 16 dependentscompcodeR - 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 2 months ago
bioconductor-package
1.38 score 97 dependenciesTitanCNA - 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
bioconductor-package
1 stars 1.16 score 82 dependenciesVariantFiltering - 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
bioconductor-package
1.24 score 169 dependenciesCoverageView - 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
bioconductor-package
1.58 score 49 dependenciesmetaMS - MS-based metabolomics annotation pipeline
MS-based metabolomics data processing and compound annotation pipeline.
Last updated 2 months ago
bioconductor-package
1.08 score 153 dependenciesFRGEpistasis - Epistasis Analysis for Quantitative Traits by Functional Regression Model
A Tool for Epistasis Analysis Based on Functional Regression Model
Last updated 2 months ago
bioconductor-package
0.82 score 48 dependenciesflowCyBar - 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
bioconductor-package
0.91 score 13 dependenciesChIPQC - Quality metrics for ChIPseq data
Quality metrics for ChIPseq data.
Last updated 2 months ago
bioconductor-package
1.00 score 158 dependenciesABSSeq - 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
bioconductor-package
1.16 score 4 dependencies 1 dependentsASSIGN - 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
bioconductor-package
1.16 score 90 dependencies 1 dependentsnondetects - Non-detects in qPCR data
Methods to model and impute non-detects in the results of qPCR experiments.
Last updated 2 months ago
bioconductor-package
1.31 score 30 dependenciesmessina - 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
bioconductor-package
0.82 score 34 dependenciesviper - 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
bioconductor-package
1.95 score 80 dependencies 5 dependentsUNDO - 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
bioconductor-package
0.71 score 5 dependenciesRcpi - 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
bioconductor-package
2.86 score 52 dependenciesQDNAseq - 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
bioconductor-package
1.85 score 50 dependencies 4 dependentsrpx - 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
bioconductor-package
1.31 score 43 dependenciesMLSeq - 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
bioconductor-package
2.05 score 135 dependencies 1 dependentsmassiR - massiR: MicroArray Sample Sex Identifier
Predicts the sex of samples in gene expression microarray datasets
Last updated 2 months ago
bioconductor-package
0.71 score 9 dependenciesINPower - 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
bioconductor-package
1.24 score 1 dependenciesCAFE - Chromosmal Aberrations Finder in Expression data
Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input
Last updated 2 months ago
bioconductor-package
0.82 score 166 dependenciesBasic4Cseq - 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
bioconductor-package
0.82 score 53 dependenciesClomial - 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
bioconductor-package
0.91 score 2 dependenciesunifiedWMWqPCR - 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
bioconductor-package
0.91 score 16 dependenciessangerseqR - 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
bioconductor-package
1.51 score 48 dependencies 2 dependentsGSCA - 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
bioconductor-package
0.91 score 64 dependenciesCOMPASS - 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
bioconductor-package
6.23 score 65 dependenciesCNEr - CNE Detection and Visualization
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
Last updated 2 months ago
bioconductor-package
3.36 score 108 dependencies 19 dependentsSomaticSignatures - 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
bioconductor-package
1.16 score 170 dependencies 1 dependentsiClusterPlus - Integrative clustering of multi-type genomic data
Integrative clustering of multiple genomic data using a joint latent variable model.
Last updated 2 months ago
bioconductor-package
1.00 score 0 dependenciesBEAT - BEAT - BS-Seq Epimutation Analysis Toolkit
Model-based analysis of single-cell methylation data
Last updated 2 months ago
bioconductor-package
0.91 score 62 dependenciesGeneOverlap - Test and visualize gene overlaps
Test two sets of gene lists and visualize the results.
Last updated 2 months ago
bioconductor-package
1.31 score 6 dependencies 1 dependentsflowBin - 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
bioconductor-package
0.91 score 29 dependenciesroar - 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
bioconductor-package
0.91 score 49 dependenciesPhenStat - Statistical analysis of phenotypic data
Package contains methods for statistical analysis of phenotypic data.
Last updated 2 months ago
bioconductor-package
1.16 score 116 dependenciesflowMatch - 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
bioconductor-package
1.80 score 11 dependenciesPECA - 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
bioconductor-package
0.82 score 78 dependenciesCRISPRseek - 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
bioconductor-package
1.45 score 98 dependencies 2 dependentsCNVrd2 - 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
bioconductor-package
0.91 score 93 dependenciesh5vc - 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
bioconductor-package
0.09 score 86 dependenciesmetaSeq - 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
bioconductor-package
0.91 score 7 dependenciesinteractiveDisplay - 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 2 months ago
bioconductor-package
1.45 score 104 dependenciesChAMP - 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
bioconductor-package
6.21 score 249 dependenciesFGNet - 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
bioconductor-package
2.35 score 24 dependencies 1 dependentsTFBSTools - 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
bioconductor-package
3.31 score 115 dependencies 18 dependentsqcmetrics - 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
bioconductor-package
1.69 score 12 dependencies 2 dependentsMSstats - 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
bioconductor-package
2.63 score 105 dependencies 6 dependentsmethylMnM - 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
bioconductor-package
1.85 score 6 dependencies 1 dependentsepivizr - 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
bioconductor-package
1.51 score 115 dependencies 2 dependentsdagLogo - 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
bioconductor-package
1.51 score 152 dependenciesbioassayR - 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
bioconductor-package
1.45 score 75 dependenciesAllelicImbalance - Investigates Allele Specific Expression
Provides a framework for allelic specific expression investigation using RNA-seq data.
Last updated 2 months ago
bioconductor-package
1.08 score 153 dependenciesrTRMui - A shiny user interface for rTRM
This package provides a web interface to compute transcriptional regulatory modules with rTRM.
Last updated 2 months ago
bioconductor-package
0.82 score 93 dependenciesomicade4 - Multiple co-inertia analysis of omics datasets
This package performes multiple co-inertia analysis of omics datasets.
Last updated 2 months ago
bioconductor-package
2.86 score 42 dependencies 1 dependentsmzID - 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
bioconductor-package
4.43 score 8 dependencies 35 dependentsBADER - 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
bioconductor-package
1.75 score 0 dependencieschipenrich - 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
bioconductor-package
1.64 score 149 dependenciesBiGGR - 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
bioconductor-package
1.80 score 21 dependenciesChemmineOB - 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
bioconductor-package
1.38 score 4 dependenciesASSET - 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
bioconductor-package
5.57 score 8 dependencies 1 dependentstrio - 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
bioconductor-package
0.82 score 10 dependenciesSpacePAC - 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
bioconductor-package
1.95 score 29 dependencies 1 dependentsSeqVarTools - 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
bioconductor-package
2.09 score 86 dependencies 2 dependentsRTN - 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
bioconductor-package
1.45 score 126 dependencies 2 dependentsrfPred - 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
bioconductor-package
1.38 score 32 dependenciesmsmsTests - 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
bioconductor-package
1.24 score 136 dependencies 1 dependentsRRHO - 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
bioconductor-package
0.71 score 5 dependenciesmsmsEDA - 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
bioconductor-package
1.69 score 132 dependencies 2 dependentsintansv - 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
bioconductor-package
1.75 score 161 dependenciesTargetScore - 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
bioconductor-package
1.85 score 3 dependenciesSigFuge - SigFuge
Algorithm for testing significance of clustering in RNA-seq data.
Last updated 2 months ago
bioconductor-package
0.91 score 49 dependenciesOmicCircos - 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
bioconductor-package
4.47 score 17 dependenciescleanUpdTSeq - 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
bioconductor-package
1.69 score 71 dependencies 1 dependentsmaPredictDSC - 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
bioconductor-package
1.00 score 127 dependenciesrTRM - 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
bioconductor-package
1.16 score 42 dependencies 1 dependentspathifier - 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
bioconductor-package
2.31 score 4 dependencies 1 dependentspaircompviz - 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
bioconductor-package
1.08 score 3 dependenciescleaver - 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
bioconductor-package
1.45 score 18 dependencies 2 dependentsflowBeads - 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
bioconductor-package
1.00 score 23 dependenciesvtpnet - variant-transcription factor-phenotype networks
variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828
Last updated 2 months ago
bioconductor-package
0.91 score 104 dependenciesEBSeq - 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
bioconductor-package
6.34 score 42 dependencies 6 dependentsXVector - 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 months ago
bioconductor-package
13.71 score 4 dependencies 1675 dependentsSplicingGraphs - 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
bioconductor-package
1.00 score 72 dependenciesBiSeq - 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
bioconductor-package
1.00 score 81 dependenciestriplex - 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
bioconductor-package
0.82 score 19 dependenciesprebs - 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
bioconductor-package
1.31 score 117 dependenciespiano - 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
bioconductor-package
3.52 score 93 dependencies 7 dependentsantiProfiles - 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
bioconductor-package
1.08 score 3 dependenciesgeNetClassifier - 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
bioconductor-package
1.80 score 11 dependencies 2 dependentsSeqGSEA - 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
bioconductor-package
0.82 score 100 dependenciesmetagenomeSeq - 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 2 months ago
bioconductor-package
2.63 score 23 dependencies 9 dependentsAnnotationHub - 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
bioconductor-package
6.32 score 58 dependencies 101 dependentsROntoTools - R Onto-Tools suite
Suite of tools for functional analysis.
Last updated 2 months ago
bioconductor-package
2.50 score 27 dependencies 2 dependentseiR - 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
bioconductor-package
0.91 score 72 dependenciesCNORfeeder - 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
bioconductor-package
1.69 score 62 dependenciesBaseSpaceR - 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
bioconductor-package
1.00 score 3 dependenciesSPEM - S-system parameter estimation method
This package can optimize the parameter in S-system models given time series data
Last updated 2 months ago
bioconductor-package
2.89 score 4 dependencies 1 dependentsSeqArray - 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
bioconductor-package
2.76 score 20 dependencies 9 dependentsRNASeqPower - Sample size for RNAseq studies
RNA-seq, sample size
Last updated 2 months ago
bioconductor-package
3.52 score 0 dependenciespathview - 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
bioconductor-package
2.83 score 45 dependencies 12 dependentsepigenomix - 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
bioconductor-package
0.82 score 97 dependenciesdeltaGseg - deltaGseg
Identifying distinct subpopulations through multiscale time series analysis
Last updated 2 months ago
bioconductor-package
0.82 score 48 dependenciesARRmNormalization - 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
bioconductor-package
1.00 score 1 dependenciesproteinProfiles - Protein Profiling
Significance assessment for distance measures of time-course protein profiles
Last updated 2 months ago
bioconductor-package
0.82 score 0 dependenciesDESeq2 - 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 2 months ago
bioconductor-package
6.71 score 65 dependencies 120 dependentscisPath - 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
bioconductor-package
0.82 score 0 dependenciesMineICA - 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
bioconductor-package
0.91 score 207 dependencieslpNet - 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
bioconductor-package
1.08 score 8 dependenciesrBiopaxParser - 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
bioconductor-package
2.22 score 2 dependenciesHTSFilter - 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
bioconductor-package
4.29 score 69 dependencies 1 dependentsMethylSeekR - Segmentation of Bis-seq data
This is a package for the discovery of regulatory regions from Bis-seq data
Last updated 2 months ago
bioconductor-package
4.17 score 74 dependenciesDrugVsDisease - 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
bioconductor-package
1.24 score 122 dependenciesclipper - 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
bioconductor-package
1.08 score 83 dependenciescasper - 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 2 months ago
bioconductor-package
1.85 score 83 dependenciesRbowtie - 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
bioconductor-package
2.46 score 0 dependencies 8 dependentsRSVSim - 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
bioconductor-package
0.91 score 54 dependenciesiBMQ - integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
Last updated 2 months ago
bioconductor-package
0.82 score 30 dependenciesGraphPAC - 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
bioconductor-package
2.00 score 44 dependencies 1 dependentsbumphunter - Bump Hunter
Tools for finding bumps in genomic data
Last updated 2 months ago
bioconductor-package
4.99 score 76 dependencies 51 dependentspvca - 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
bioconductor-package
2.31 score 44 dependencies 1 dependentsBiocParallel - 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
bioconductor-package
12.32 score 8 dependencies 1069 dependentsUniProt.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
bioconductor-package
2.05 score 61 dependencies 3 dependentsSNAGEE - 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
bioconductor-package
0.82 score 1 dependenciesilluminaio - Parsing Illumina Microarray Output Files
Tools for parsing Illumina's microarray output files, including IDAT.
Last updated 2 months ago
bioconductor-package
4.63 score 4 dependencies 44 dependentsmatchBox - 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
bioconductor-package
1.00 score 0 dependenciesVariantTools - Tools for Exploratory Analysis of Variant Calls
Explore, diagnose, and compare variant calls using filters.
Last updated 2 months ago
bioconductor-package
1.31 score 70 dependencies 1 dependentsNOISeq - 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
bioconductor-package
6.30 score 4 dependencies 4 dependentsTransView - 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 2 months ago
bioconductor-package
1.16 score 23 dependenciesHTSeqGenie - A NGS analysis pipeline.
Libraries to perform NGS analysis.
Last updated 2 months ago
bioconductor-package
1.08 score 85 dependenciesHMMcopy - 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
bioconductor-package
3.31 score 1 dependencies 1 dependentsCNORode - ODE add-on to CellNOptR
Logic based ordinary differential equation (ODE) add-on to CellNOptR.
Last updated 2 months ago
bioconductor-package
1.75 score 63 dependencies 1 dependentsCNORdt - 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
bioconductor-package
1.00 score 63 dependenciesagilp - Agilent expression array processing package
More about what it does (maybe more than one line)
Last updated 2 months ago
bioconductor-package
1.58 score 0 dependenciesDeconRNASeq - 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
bioconductor-package
0.91 score 35 dependencieshpar - 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
bioconductor-package
2.22 score 60 dependencies 1 dependentsOrganismDbi - 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
bioconductor-package
4.40 score 96 dependencies 37 dependentslmdme - 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
bioconductor-package
1.58 score 4 dependenciesfmcsR - 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
bioconductor-package
2.05 score 69 dependencies 1 dependentsCNORfuzzy - 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
bioconductor-package
1.38 score 63 dependenciesGeneNetworkBuilder - 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
bioconductor-package
1.00 score 34 dependenciesMotifDb - 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
bioconductor-package
3.26 score 51 dependencies 1 dependentsChIPXpress - 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
bioconductor-package
0.91 score 94 dependenciesPADOG - 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
bioconductor-package
1.51 score 53 dependencies 2 dependentsiPAC - 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
bioconductor-package
3.16 score 28 dependencies 3 dependentsgmapR - 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
bioconductor-package
1.58 score 70 dependencies 1 dependentsbsseq - Analyze, manage and store bisulfite sequencing data
A collection of tools for analyzing and visualizing bisulfite sequencing data.
Last updated 2 months ago
bioconductor-package
5.02 score 78 dependencies 16 dependentssynapter - 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
bioconductor-package
1.24 score 141 dependenciesPWMEnrich - 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
bioconductor-package
3.16 score 22 dependenciesDSS - 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
bioconductor-package
2.14 score 79 dependencies 5 dependentsflowPeaks - 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 2 months ago
bioconductor-package
1.58 score 0 dependencies 2 dependentsannmap - 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
bioconductor-package
1.85 score 61 dependenciesrols - 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
bioconductor-package
2.14 score 17 dependencies 3 dependentsMiRaGE - 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
bioconductor-package
1.31 score 39 dependenciesstaRank - Stability Ranking
Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.
Last updated 9 months ago
bioconductor-package
0.82 score 82 dependenciescancerclass - 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
bioconductor-package
1.00 score 3 dependenciesDirichletMultinomial - 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
bioconductor-package
3.78 score 3 dependencies 26 dependentscategoryCompare - 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
bioconductor-package
2.80 score 83 dependenciesMinimumDistance - 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
bioconductor-package
1.58 score 87 dependenciesiASeq - 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
bioconductor-package
0.91 score 0 dependenciesEBcoexpress - 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
bioconductor-package
1.85 score 8 dependenciesHiTC - 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
bioconductor-package
1.08 score 50 dependenciescnvGSA - 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
bioconductor-package
0.91 score 25 dependenciesiBBiG - 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
bioconductor-package
1.38 score 47 dependencies 2 dependentsReactomePA - 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
bioconductor-package
2.53 score 121 dependencies 7 dependentsHybridMTest - 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
bioconductor-package
1.85 score 7 dependencies 1 dependentscoGPS - 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
bioconductor-package
0.82 score 0 dependenciesffpe - 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
bioconductor-package
1.38 score 155 dependenciesBRAIN - 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
bioconductor-package
2.57 score 21 dependenciesPING - 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
bioconductor-package
4.28 score 164 dependenciesgwascat - 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
bioconductor-package
2.09 score 99 dependencies 2 dependentsternarynet - 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
bioconductor-package
1.08 score 19 dependenciesGviz - 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
bioconductor-package
4.79 score 146 dependencies 45 dependentsdeepSNV - 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
bioconductor-package
1.38 score 71 dependencies 1 dependentsphyloseq - 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
bioconductor-package
4.89 score 72 dependencies 48 dependentsDART - 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
bioconductor-package
6.19 score 11 dependenciesBAGS - 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
bioconductor-package
1.00 score 3 dependenciesrhdf5 - 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 2 months ago
bioconductor-package
8.05 score 2 dependencies 219 dependentseasyRNASeq -
Last updated 2 months ago
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
bioconductor-package
1.08 score 59 dependenciesmaskBAD - Masking probes with binding affinity differences
Package includes functions to analyze and mask microarray expression data.
Last updated 2 months ago
bioconductor-package
1.38 score 24 dependenciesAffyRNADegradation - 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
bioconductor-package
2.05 score 7 dependenciesASEB - 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
bioconductor-package
1.08 score 0 dependenciesBiocGenerics - S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Last updated 2 months ago
bioconductor-package
14.57 score 0 dependencies 2182 dependentsncdfFlow - 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
bioconductor-package
3.08 score 12 dependencies 11 dependentstweeDEseq - 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
bioconductor-package
1.95 score 16 dependencies 1 dependentsCellNOptR - 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
bioconductor-package
2.38 score 61 dependencies 6 dependentsisobar - 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
bioconductor-package
1.80 score 82 dependenciesggbio - 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
bioconductor-package
3.43 score 160 dependencies 19 dependentsr3Cseq - 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
bioconductor-package
0.91 score 95 dependenciesminfi - Analyze Illumina Infinium DNA methylation arrays
Tools to analyze & visualize Illumina Infinium methylation arrays.
Last updated 2 months ago
bioconductor-package
4.44 score 129 dependencies 34 dependentsGWASTools - 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
bioconductor-package
3.58 score 84 dependencies 5 dependentscummeRbund - 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
bioconductor-package
5.81 score 150 dependenciesCNAnorm - 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
bioconductor-package
3.43 score 1 dependenciesbiovizBase - 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
bioconductor-package
5.60 score 125 dependencies 74 dependentsAGDEX - Agreement of Differential Expression Analysis
A tool to evaluate agreement of differential expression for cross-species genomics
Last updated 2 months ago
bioconductor-package
0.82 score 43 dependenciesDiffBind - 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
bioconductor-package
6.26 score 138 dependencies 2 dependentsdks - 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
bioconductor-package
1.08 score 2 dependenciesEDASeq - 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
bioconductor-package
5.51 score 108 dependencies 9 dependentsDTA - 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
bioconductor-package
3.47 score 2 dependencies 1 dependentsRTopper - 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
bioconductor-package
0.91 score 9 dependenciesPANR - 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
bioconductor-package
1.08 score 22 dependenciesweaver - 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
bioconductor-package
1.00 score 2 dependenciesgraphite - 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
bioconductor-package
3.47 score 42 dependencies 20 dependentsGeneExpressionSignature - 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
bioconductor-package
0.91 score 2 dependenciesmzR - 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 2 months ago
bioconductor-package
4.72 score 6 dependencies 41 dependentsrqubic - 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
bioconductor-package
1.08 score 43 dependencies 1 dependentsPREDA - Position Related Data Analysis
Package for the position related analysis of quantitative functional genomics data.
Last updated 2 months ago
bioconductor-package
1.85 score 48 dependenciesVariantAnnotation - Annotation of Genetic Variants
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Last updated 2 months ago
bioconductor-package
7.20 score 69 dependencies 152 dependentsStreamer - 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
bioconductor-package
1.08 score 4 dependenciesNormqPCR - 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
bioconductor-package
4.13 score 40 dependenciesnucleR - Nucleosome positioning package for R
Nucleosome positioning for Tiling Arrays and NGS experiments.
Last updated 2 months ago
bioconductor-package
1.16 score 80 dependenciesRedeR - 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
bioconductor-package
2.46 score 19 dependencies 7 dependentsGRENITS - 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
bioconductor-package
1.00 score 34 dependenciesCormotif - Correlation Motif Fit
It fits correlation motif model to multiple studies to detect study specific differential expression patterns.
Last updated 2 months ago
bioconductor-package
0.82 score 9 dependenciesReadqPCR - Read qPCR data
The package provides functions to read raw RT-qPCR data of different platforms.
Last updated 2 months ago
bioconductor-package
2.83 score 2 dependencies 1 dependentsRepitools - 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
bioconductor-package
0.91 score 65 dependenciescqn - Conditional quantile normalization
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
Last updated 2 months ago
bioconductor-package
3.24 score 10 dependencies 4 dependentsrandPack - Randomization routines for Clinical Trials
A suite of classes and functions for randomizing patients in clinical trials.
Last updated 2 months ago
bioconductor-package
1.16 score 2 dependenciesDEXSeq - 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
bioconductor-package
2.42 score 108 dependencies 6 dependentsREDseq - 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
bioconductor-package
1.08 score 124 dependenciesflowWorkspace - 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
bioconductor-package
2.94 score 57 dependencies 10 dependentsa4 - 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
bioconductor-package
1.16 score 77 dependenciesa4Reporting - 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
bioconductor-package
1.24 score 1 dependencies 1 dependentsa4Core - Automated Affymetrix Array Analysis Core Package
Utility functions for the Automated Affymetrix Array Analysis set of packages.
Last updated 2 months ago
bioconductor-package
1.85 score 12 dependencies 4 dependentsa4Classif - 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
bioconductor-package
1.31 score 24 dependencies 1 dependentsa4Preproc - 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
bioconductor-package
1.64 score 2 dependencies 3 dependentsa4Base - 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
bioconductor-package
1.38 score 69 dependencies 1 dependentsNCIgraph - 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
bioconductor-package
1.45 score 49 dependencies 1 dependentssurvcomp - Performance Assessment and Comparison for Survival Analysis
Assessment and Comparison for Performance of Risk Prediction (Survival) Models.
Last updated 2 months ago
bioconductor-package
6.48 score 30 dependencies 12 dependentsgenefu - 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 2 months ago
bioconductor-package
4.74 score 103 dependencies 3 dependentsRsubread - 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 2 months ago
bioconductor-package
6.48 score 2 dependencies 9 dependentscn.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
bioconductor-package
1.08 score 57 dependenciesflowPlots - 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
bioconductor-package
0.82 score 0 dependenciesibh - 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
bioconductor-package
0.91 score 1 dependenciesclusterProfiler - 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 2 months ago
bioconductor-package
4.97 score 118 dependencies 44 dependentsclstutils - Tools for performing taxonomic assignment
Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.
Last updated 2 months ago
bioconductor-package
0.91 score 29 dependenciesclst - 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
bioconductor-package
1.00 score 7 dependencies 1 dependentsRNAinteract - Estimate Pairwise Interactions from multidimensional features
RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis.
Last updated 9 months ago
bioconductor-package
0.91 score 103 dependenciesprocoil - 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
bioconductor-package
1.00 score 29 dependenciespvac - 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
bioconductor-package
1.16 score 7 dependencieschopsticks - The 'snp.matrix' and 'X.snp.matrix' Classes
Implements classes and methods for large-scale SNP association studies
Last updated 2 months ago
bioconductor-package
1.08 score 3 dependenciesmosaics - 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
bioconductor-package
0.82 score 44 dependenciesExiMiR - 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
bioconductor-package
1.58 score 9 dependenciesphenoTest - 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
bioconductor-package
1.16 score 137 dependencies 1 dependentsmgsa - 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
bioconductor-package
1.95 score 5 dependenciesTurboNorm - 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
bioconductor-package
0.91 score 12 dependenciesTEQC - 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
bioconductor-package
3.16 score 33 dependenciesMLP - 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
bioconductor-package
4.40 score 43 dependencies 1 dependentsDEGraph - 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
bioconductor-package
1.00 score 57 dependenciesMEDIPS - 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
bioconductor-package
1.00 score 100 dependenciesADaCGH2 - 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
bioconductor-package
1.00 score 89 dependenciesR453Plus1Toolbox - 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
bioconductor-package
0.91 score 108 dependenciesGeneGA - 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
bioconductor-package
0.71 score 11 dependenciesCRImage - 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
bioconductor-package
1.80 score 53 dependenciesiSeq - 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
bioconductor-package
2.89 score 0 dependenciesnetresponse - 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
bioconductor-package
1.00 score 66 dependenciesOTUbase - Provides structure and functions for the analysis of OTU data
Provides a platform for Operational Taxonomic Unit based analysis
Last updated 2 months ago
bioconductor-package
0.91 score 59 dependenciesles - 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
bioconductor-package
1.08 score 8 dependencies 1 dependentsMulcom - Calculates Mulcom test
Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test.
Last updated 2 months ago
bioconductor-package
1.16 score 8 dependenciesRDRToolbox - 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
bioconductor-package
0.91 score 30 dependenciesBioNet - 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
bioconductor-package
4.55 score 45 dependencies 2 dependentsMBCB - 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
bioconductor-package
1.45 score 2 dependenciesNTW - 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
bioconductor-package
1.45 score 1 dependenciesattract - 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
bioconductor-package
1.31 score 63 dependenciesaffyILM - 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
bioconductor-package
0.82 score 25 dependenciesgenomes - Genome sequencing project metadata
Download genome and assembly reports from NCBI
Last updated 2 months ago
bioconductor-package
0.71 score 26 dependenciesflowTrans - Parameter Optimization for Flow Cytometry Data Transformation
Profile maximum likelihood estimation of parameters for flow cytometry data transformations.
Last updated 2 months ago
bioconductor-package
2.09 score 26 dependenciesGSRI - 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
bioconductor-package
0.82 score 58 dependenciesGEOsubmission - 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
bioconductor-package
0.82 score 7 dependenciesPROMISE - 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
bioconductor-package
6.22 score 43 dependencies 1 dependentsflowMeans - 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
bioconductor-package
3.31 score 30 dependencies 2 dependentsPICS - Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.
Last updated 2 months ago
bioconductor-package
5.60 score 42 dependencies 1 dependentstigre - 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
bioconductor-package
1.45 score 46 dependenciesRsamtools - 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 2 months ago
bioconductor-package
10.44 score 30 dependencies 562 dependentsgirafe - 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 2 months ago
bioconductor-package
1.24 score 56 dependenciesBeadDataPackR - 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
bioconductor-package
2.14 score 0 dependencies 5 dependentsgenoCN - 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
bioconductor-package
0.71 score 0 dependenciesSamSPECTRAL -
Last updated 2 months ago
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
bioconductor-package
1.00 score 51 dependenciesiChip - 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
bioconductor-package
2.14 score 2 dependenciesConsensusClusterPlus - ConsensusClusterPlus
algorithm for determining cluster count and membership by stability evidence in unsupervised analysis
Last updated 2 months ago
bioconductor-package
1 stars 3.47 score 4 dependencies 21 dependentshyperdraw - Visualizing Hypergaphs
Functions for visualizing hypergraphs.
Last updated 2 months ago
bioconductor-package
1.38 score 4 dependencies 1 dependentsfrmaTools - Frozen RMA Tools
Tools for advanced use of the frma package.
Last updated 2 months ago
bioconductor-package
0.71 score 8 dependenciesfrma - Frozen RMA and Barcode
Preprocessing and analysis for single microarrays and microarray batches.
Last updated 2 months ago
bioconductor-package
3.80 score 57 dependencies 1 dependentsCSAR - 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
bioconductor-package
3.00 score 17 dependenciesSpeCond - 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
bioconductor-package
1.51 score 11 dependenciesDEGseq - 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
bioconductor-package
1.00 score 34 dependenciesLiquidAssociation - 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
bioconductor-package
1.16 score 57 dependencies 1 dependentsHTqPCR - Automated analysis of high-throughput qPCR data
Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).
Last updated 2 months ago
bioconductor-package
4.91 score 15 dependencies 2 dependentsChIPseqR - 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
bioconductor-package
1.08 score 62 dependenciesChromHeatMap - 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
bioconductor-package
1.08 score 69 dependenciescycle - 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
bioconductor-package
0.82 score 10 dependenciesCGHnormaliter - 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
bioconductor-package
2.09 score 11 dependenciesRTCA - 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
bioconductor-package
6.20 score 4 dependenciesAgiMicroRna - Processing and Differential Expression Analysis of Agilent microRNA chips
Processing and Analysis of Agilent microRNA data
Last updated 2 months ago
bioconductor-package
4.31 score 197 dependenciesclippda - 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
bioconductor-package
1.08 score 35 dependenciesMiChip - 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
bioconductor-package
0.71 score 2 dependenciesChIPsim - 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
bioconductor-package
1.24 score 54 dependenciesmBPCR - 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
bioconductor-package
1.75 score 112 dependenciesRPA - 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
bioconductor-package
1.16 score 97 dependencies 1 dependentsBUS - 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
bioconductor-package
0.71 score 2 dependenciesflowFP - 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
bioconductor-package
1.38 score 24 dependencies 2 dependentsflowMerge - 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
bioconductor-package
1.31 score 37 dependencies 1 dependentschipseq - chipseq: A package for analyzing chipseq data
Tools for helping process short read data for chipseq experiments.
Last updated 2 months ago
bioconductor-package
2.97 score 54 dependencies 5 dependentsCNTools - 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
bioconductor-package
1.08 score 47 dependencies 1 dependentsmethylumi - 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
bioconductor-package
6.02 score 144 dependencies 16 dependentsRmagpie - 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
bioconductor-package
0.71 score 12 dependenciesflowStats - 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
bioconductor-package
1.64 score 92 dependencies 1 dependentsqpcrNorm - 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
bioconductor-package
1.24 score 9 dependenciescrlmm - 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
bioconductor-package
2.50 score 63 dependencies 3 dependentsGeneSelectMMD - 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
bioconductor-package
1.45 score 5 dependencies 1 dependentsgenomeIntervals - 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
bioconductor-package
2.27 score 18 dependencies 3 dependentsCAMERA - 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
bioconductor-package
9.74 score 150 dependencies 6 dependentsmetahdep - 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
bioconductor-package
0.91 score 0 dependenciesSPIA - 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
bioconductor-package
1.75 score 7 dependencies 4 dependentsspkTools - 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
bioconductor-package
1.08 score 4 dependenciesqpgraph - 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
bioconductor-package
1.58 score 74 dependencies 2 dependentsKEGGgraph - 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
bioconductor-package
5.35 score 6 dependencies 26 dependentsGOSemSim - 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
bioconductor-package
5.55 score 43 dependencies 68 dependentsflagme - Analysis of Metabolomics GC/MS Data
Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.
Last updated 2 months ago
bioconductor-package
1.24 score 158 dependenciesHilbertVisGUI -
Last updated 2 months ago
HilbertVis - Hilbert curve visualization
Functions to visualize long vectors of integer data by means of Hilbert curves
Last updated 2 months ago
bioconductor-package
1.16 score 1 dependencies 1 dependentsBicARE - Biclustering Analysis and Results Exploration
Biclustering Analysis and Results Exploration.
Last updated 2 months ago
bioconductor-package
1.51 score 49 dependencies 2 dependentsarrayMvout - 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
bioconductor-package
0.91 score 156 dependenciesaffyContam - structured corruption of affymetrix cel file data
structured corruption of cel file data to demonstrate QA effectiveness
Last updated 2 months ago
bioconductor-package
1.16 score 8 dependencies 1 dependentsxmapbridge - 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
bioconductor-package
0.71 score 0 dependenciesparody - 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
bioconductor-package
1.16 score 0 dependencies 1 dependentsChemmineR - 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
bioconductor-package
2.92 score 67 dependencies 12 dependentsKCsmart - Multi sample aCGH analysis package using kernel convolution
Multi sample aCGH analysis package using kernel convolution
Last updated 2 months ago
bioconductor-package
1.31 score 10 dependenciesArrayExpress - 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
bioconductor-package
6.25 score 57 dependencies 1 dependentsmicroRNA - Data and functions for dealing with microRNAs
Different data resources for microRNAs and some functions for manipulating them.
Last updated 2 months ago
bioconductor-package
5.26 score 18 dependenciesMEDME - 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
bioconductor-package
3.33 score 85 dependenciesPLPE - 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
bioconductor-package
0.71 score 4 dependenciesDFP - 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
bioconductor-package
1.51 score 2 dependenciesiterativeBMAsurv - 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
bioconductor-package
1.08 score 11 dependenciesITALICS - ITALICS
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
Last updated 2 months ago
bioconductor-package
2.00 score 61 dependenciesiterativeBMA - 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
bioconductor-package
0.82 score 13 dependenciesminet - Mutual Information NETworks
This package implements various algorithms for inferring mutual information networks from data.
Last updated 2 months ago
bioconductor-package
4.94 score 1 dependencies 16 dependentsmultiscan - R package for combining multiple scans
Estimates gene expressions from several laser scans of the same microarray
Last updated 2 months ago
bioconductor-package
1.95 score 2 dependenciesmiRNApath - 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
bioconductor-package
2.83 score 0 dependenciesSIM - Integrated Analysis on two human genomic datasets
Finds associations between two human genomic datasets.
Last updated 2 months ago
bioconductor-package
1.00 score 50 dependenciesHELP - 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
bioconductor-package
0.71 score 2 dependenciesCMA - 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
bioconductor-package
6.21 score 2 dependenciesCGHregions - 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
bioconductor-package
1.75 score 6 dependenciesCGHbase - CGHbase: Base functions and classes for arrayCGH data analysis.
Contains functions and classes that are needed by arrayCGH packages.
Last updated 2 months ago
bioconductor-package
2.31 score 5 dependencies 8 dependentsShortRead - 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
bioconductor-package
4.97 score 53 dependencies 51 dependentsgoProfiles - 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
bioconductor-package
2.60 score 43 dependencies 1 dependentsRBioinf - RBioinf
Functions and datasets and examples to accompany the monograph R For Bioinformatics.
Last updated 2 months ago
bioconductor-package
0.71 score 2 dependenciesGEOmetadb -
Last updated 2 months ago
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
bioconductor-package
2.31 score 12 dependencies 6 dependentsGSEAlm - 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
bioconductor-package
2.05 score 2 dependenciessnpStats - 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
bioconductor-package
5.37 score 5 dependencies 16 dependentsBCRANK - 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
bioconductor-package
2.00 score 18 dependenciesmdqc - 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
bioconductor-package
1.00 score 2 dependencies 1 dependentsGraphAlignment - 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
bioconductor-package
1.75 score 0 dependenciesXDE - 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
bioconductor-package
1.90 score 55 dependenciesgaga - 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
bioconductor-package
1.64 score 9 dependencies 1 dependentsRtreemix - 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
bioconductor-package
0.82 score 68 dependenciesrsbml - 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
bioconductor-package
1.80 score 2 dependencies 1 dependentsVanillaICE - 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
bioconductor-package
1.24 score 85 dependencies 1 dependentsoligoClasses - 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
bioconductor-package
3.33 score 51 dependencies 19 dependentsCGHcall - 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
bioconductor-package
1.95 score 10 dependencies 6 dependentsarrayQualityMetrics - 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
bioconductor-package
6.21 score 126 dependenciesvbmp - 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
bioconductor-package
0.82 score 0 dependencieskeggorthology - 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
bioconductor-package
1.00 score 41 dependenciesbiocGraph - 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
bioconductor-package
1.16 score 46 dependenciesGSEABase - 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
bioconductor-package
5.72 score 42 dependencies 78 dependentsbgx - Bayesian Gene eXpression
Bayesian integrated analysis of Affymetrix GeneChips
Last updated 2 months ago
bioconductor-package
1.24 score 25 dependenciesrbsurv - Robust likelihood-based survival modeling with microarray data
This package selects genes associated with survival.
Last updated 2 months ago
bioconductor-package
0.91 score 5 dependenciesGeneticsPed - 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
bioconductor-package
1.31 score 6 dependenciesMassSpecWavelet - 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 2 months ago
bioconductor-package
4.25 score 0 dependencies 16 dependentsACME - 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
bioconductor-package
5.27 score 2 dependenciesSLqPCR - 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
bioconductor-package
3.06 score 0 dependenciesLBE - 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
bioconductor-package
1.08 score 0 dependencies 1 dependentsannotationTools - 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
bioconductor-package
0.82 score 2 dependenciestopGO - 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
bioconductor-package
6.56 score 43 dependencies 18 dependentsseqLogo - 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
bioconductor-package
4.95 score 0 dependencies 29 dependentsBufferedMatrixMethods - Microarray Data related methods that utlize BufferedMatrix objects
Microarray analysis methods that use BufferedMatrix objects
Last updated 2 months ago
bioconductor-package
0.82 score 1 dependenciesBufferedMatrix - 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 2 months ago
bioconductor-package
1.16 score 0 dependencies 1 dependentslumi - 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
bioconductor-package
6.38 score 150 dependencies 9 dependentsoccugene - 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
bioconductor-package
0.82 score 0 dependenciesAnnotationDbi - Manipulation of SQLite-based annotations in Bioconductor
Implements a user-friendly interface for querying SQLite-based annotation data packages.
Last updated 2 months ago
bioconductor-package
11.58 score 37 dependencies 766 dependentsflowViz - Visualization for flow cytometry
Provides visualization tools for flow cytometry data.
Last updated 2 months ago
bioconductor-package
4.38 score 23 dependencies 12 dependentsflowCore - 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
bioconductor-package
5.22 score 10 dependencies 56 dependentsRbcBook1 - Support for Springer monograph on Bioconductor
tools for building book
Last updated 2 months ago
bioconductor-package
0.82 score 4 dependenciespcaMethods - 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
bioconductor-package
5.51 score 4 dependencies 70 dependentssplots - 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
bioconductor-package
1.64 score 1 dependencies 3 dependentslapmix - 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
bioconductor-package
0.82 score 2 dependenciesBioMVCClass - Model-View-Controller (MVC) Classes That Use Biobase
Creates classes used in model-view-controller (MVC) design
Last updated 2 months ago
bioconductor-package
0.82 score 5 dependenciesspikeLI - 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
bioconductor-package
0.71 score 0 dependenciesaroma.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
bioconductor-package
3.38 score 4 dependencies 20 dependentsquantsmooth - 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
bioconductor-package
2.53 score 7 dependencies 7 dependentsHarshlight - 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
bioconductor-package
2.27 score 27 dependenciesABarray - 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
bioconductor-package
1.64 score 7 dependencieslogicFS - 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
bioconductor-package
1.38 score 5 dependenciesOrderedList - 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
bioconductor-package
2.60 score 3 dependenciescghMCR - 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
bioconductor-package
0.82 score 51 dependenciesmaCorrPlot - Visualize artificial correlation in microarray data
Graphically displays correlation in microarray data that is due to insufficient normalization
Last updated 2 months ago
bioconductor-package
0.82 score 1 dependenciesHeatplus - 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
bioconductor-package
5.79 score 1 dependencies 5 dependentsOCplus - 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
bioconductor-package
2.05 score 11 dependenciesEBImage - 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
bioconductor-package
4.00 score 37 dependencies 29 dependentssizepower - 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
bioconductor-package
0.82 score 0 dependenciescopa - 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
bioconductor-package
1.31 score 2 dependenciesadSplit - 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
bioconductor-package
0.82 score 45 dependenciescodelink - 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
bioconductor-package
1.69 score 43 dependenciesGEOquery - 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
bioconductor-package
5.18 score 41 dependencies 57 dependentspathRender - Render molecular pathways
build graphs from pathway databases, render them by Rgraphviz.
Last updated 2 months ago
bioconductor-package
1.08 score 42 dependenciespanp - 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
bioconductor-package
1.51 score 7 dependenciesMantelCorr - 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
bioconductor-package
0.91 score 0 dependenciesMANOR - 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
bioconductor-package
1.31 score 4 dependenciesaffycoretools - 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
bioconductor-package
1.16 score 196 dependencies 1 dependentsmaSigPro - 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
bioconductor-package
6.20 score 6 dependenciesbiocViews - 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
bioconductor-package
3.11 score 10 dependencies 14 dependentsaffxparser - 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
bioconductor-package
3.08 score 0 dependencies 15 dependentstimecourse - 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
bioconductor-package
1.64 score 6 dependenciesdiffGeneAnalysis - Performs differential gene expression Analysis
Analyze microarray data
Last updated 2 months ago
bioconductor-package
1.58 score 1 dependenciesfdrame - 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
bioconductor-package
0.91 score 0 dependenciesclusterStab - 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
bioconductor-package
0.82 score 2 dependenciesGeneMeta - MetaAnalysis for High Throughput Experiments
A collection of meta-analysis tools for analysing high throughput experimental data
Last updated 2 months ago
bioconductor-package
1.16 score 47 dependencies 1 dependentsCategory - Category Analysis
A collection of tools for performing category (gene set enrichment) analysis.
Last updated 2 months ago
bioconductor-package
4.59 score 51 dependencies 22 dependentshypergraph - A package providing hypergraph data structures
A package that implements some simple capabilities for representing and manipulating hypergraphs.
Last updated 2 months ago
bioconductor-package
1.95 score 2 dependencies 4 dependentsssize - Estimate Microarray Sample Size
Functions for computing and displaying sample size information for gene expression arrays.
Last updated 2 months ago
bioconductor-package
1.90 score 3 dependenciesgeneRecommender - 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
bioconductor-package
1.00 score 2 dependenciesidiogram - idiogram
A package for plotting genomic data by chromosomal location
Last updated 2 months ago
bioconductor-package
0.82 score 42 dependenciesMiPP - Misclassification Penalized Posterior Classification
This package finds optimal sets of genes that seperate samples into two or more classes.
Last updated 2 months ago
bioconductor-package
1.38 score 6 dependenciesRankProd - 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
bioconductor-package
1.90 score 2 dependencies 5 dependentsplgem - 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
bioconductor-package
1.24 score 3 dependencies 1 dependentssafe - 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
bioconductor-package
2.00 score 39 dependencies 5 dependentsmade4 - 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
bioconductor-package
5.95 score 41 dependencies 2 dependentsplier - 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
bioconductor-package
2.00 score 7 dependenciesapComplex - 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
bioconductor-package
1.58 score 43 dependenciesCoCiteStats - Different test statistics based on co-citation.
A collection of software tools for dealing with co-citation data.
Last updated 2 months ago
bioconductor-package
1.38 score 39 dependenciesbioDist - Different distance measures
A collection of software tools for calculating distance measures.
Last updated 2 months ago
bioconductor-package
3.16 score 3 dependencies 2 dependentssagenhaft - 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
bioconductor-package
1.08 score 1 dependenciesSBMLR - SBML-R Interface and Analysis Tools
This package contains a systems biology markup language (SBML) interface to R.
Last updated 2 months ago
bioconductor-package
2.09 score 2 dependenciesMVCClass - Model-View-Controller (MVC) Classes
Creates classes used in model-view-controller (MVC) design
Last updated 2 months ago
bioconductor-package
1.16 score 0 dependencies 1 dependentsstepNorm - Stepwise normalization functions for cDNA microarrays
Stepwise normalization functions for cDNA microarray data.
Last updated 2 months ago
bioconductor-package
0.82 score 4 dependenciesOLINgui - Graphical user interface for OLIN
Graphical user interface for the OLIN package
Last updated 2 months ago
bioconductor-package
1.24 score 9 dependencieshopach - 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
bioconductor-package
2.70 score 3 dependencies 5 dependentsGLAD - 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
bioconductor-package
5.84 score 3 dependencies 3 dependentsgenArise - 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
bioconductor-package
0.71 score 4 dependenciesnnNorm - 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
bioconductor-package
0.71 score 4 dependenciesMLInterfaces - 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
bioconductor-package
3.16 score 114 dependencies 6 dependentsOLIN - 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
bioconductor-package
1.00 score 5 dependencies 1 dependentsglobaltest - 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
bioconductor-package
2.27 score 44 dependencies 7 dependentsGraphAT - Graph Theoretic Association Tests
Functions and data used in Balasubramanian, et al. (2004)
Last updated 2 months ago
bioconductor-package
1.08 score 12 dependenciesHEM - 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
bioconductor-package
3.82 score 2 dependenciesaCGH - 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
bioconductor-package
1.80 score 8 dependencies 4 dependentsGOstats - 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
bioconductor-package
3.06 score 57 dependencies 14 dependentsDNAcopy - 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
bioconductor-package
5.34 score 0 dependencies 64 dependentsconvert - Convert Microarray Data Objects
Define coerce methods for microarray data objects.
Last updated 2 months ago
bioconductor-package
1.24 score 5 dependencies 1 dependentsmarray - 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
bioconductor-package
6.19 score 2 dependencies 38 dependentslimmaGUI - 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
bioconductor-package
1.00 score 5 dependenciesaffylmGUI - 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
bioconductor-package
4.02 score 49 dependenciesgoTools - Functions for Gene Ontology database
Wraper functions for description/comparison of oligo ID list using Gene Ontology database
Last updated 2 months ago
bioconductor-package
0.71 score 39 dependenciesarrayQuality - Assessing array quality on spotted arrays
Functions for performing print-run and array level quality assessment.
Last updated 2 months ago
bioconductor-package
2.50 score 7 dependenciesaltcdfenvs - alternative CDF environments (aka probeset mappings)
Convenience data structures and functions to handle cdfenvs
Last updated 2 months ago
bioconductor-package
2.05 score 26 dependencies 1 dependentsPROcess - Ciphergen SELDI-TOF Processing
A package for processing protein mass spectrometry data.
Last updated 2 months ago
bioconductor-package
2.97 score 4 dependenciesEBarrays - 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
bioconductor-package
4.07 score 4 dependencies 6 dependentsIcens - NPMLE for Censored and Truncated Data
Many functions for computing the NPMLE for censored and truncated data.
Last updated 2 months ago
bioconductor-package
2.35 score 3 dependencies 7 dependentsimpute - impute: Imputation for microarray data
Imputation for microarray data (currently KNN only)
Last updated 2 months ago
bioconductor-package
6.77 score 0 dependencies 130 dependentspickgene - Adaptive Gene Picking for Microarray Expression Data Analysis
Functions to Analyze Microarray (Gene Expression) Data.
Last updated 2 months ago
bioconductor-package
0.82 score 1 dependenciesLPE - 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
bioconductor-package
1.75 score 0 dependencies 1 dependentsecolitk - 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
bioconductor-package
0.82 score 2 dependencieswebbioc - 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
bioconductor-package
1.00 score 77 dependenciesRBGL - 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
bioconductor-package
6.97 score 3 dependencies 140 dependentsaffyPLM - 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 2 months ago
bioconductor-package
1.69 score 24 dependencies 4 dependentsfactDesign - 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
bioconductor-package
1.00 score 2 dependenciesMeasurementError.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
bioconductor-package
0.91 score 0 dependenciesgpls - 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
bioconductor-package
1.00 score 0 dependenciesdaMA - 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
bioconductor-package
0.91 score 1 dependenciesannaffy - 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
bioconductor-package
2.18 score 40 dependencies 3 dependentssiggenes - 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
bioconductor-package
6.44 score 8 dependencies 40 dependentsgcrma - Background Adjustment Using Sequence Information
Background adjustment using sequence information
Last updated 2 months ago
bioconductor-package
6.44 score 23 dependencies 12 dependentsaffycomp - 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
bioconductor-package
1.00 score 2 dependenciesRgraphviz - 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
bioconductor-package
7.03 score 2 dependencies 112 dependentswidgetTools - Creates an interactive tcltk widget
This packages contains tools to support the construction of tcltk widgets
Last updated 2 months ago
bioconductor-package
2.35 score 0 dependencies 8 dependentsmakecdfenv - 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
bioconductor-package
2.80 score 7 dependencies 2 dependentsgraph - graph: A package to handle graph data structures
A package that implements some simple graph handling capabilities.
Last updated 2 months ago
bioconductor-package
9.42 score 1 dependencies 339 dependentsaffy - 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
bioconductor-package
7.85 score 6 dependencies 107 dependentspreprocessCore - A collection of pre-processing functions
A library of core preprocessing routines.
Last updated 2 months ago
bioconductor-package
1 stars 8.94 score 0 dependencies 222 dependentsaffyio - 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 2 months ago
bioconductor-package
6.66 score 1 dependencies 119 dependentstkWidgets - R based tk widgets
Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.
Last updated 2 months ago
bioconductor-package
2.05 score 2 dependencies 6 dependentsROC - utilities for ROC, with microarray focus
Provide utilities for ROC, with microarray focus.
Last updated 2 months ago
bioconductor-package
2.53 score 5 dependencies 10 dependentsctc - Cluster and Tree Conversion.
Tools for export and import classification trees and clusters to other programs
Last updated 2 months ago
bioconductor-package
2.09 score 1 dependencies 2 dependentsgeneplotter - Graphics related functions for Bioconductor
Functions for plotting genomic data
Last updated 2 months ago
bioconductor-package
3.76 score 43 dependencies 12 dependentsgenefilter - genefilter: methods for filtering genes from high-throughput experiments
Some basic functions for filtering genes.
Last updated 2 months ago
bioconductor-package
8.38 score 46 dependencies 155 dependentsannotate - Annotation for microarrays
Using R enviroments for annotation.
Last updated 2 months ago
bioconductor-package
8.34 score 40 dependencies 253 dependentsDynDoc - Dynamic document tools
A set of functions to create and interact with dynamic documents and vignettes.
Last updated 2 months ago
bioconductor-package
2.14 score 0 dependencies 7 dependentsBiobase - Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
Last updated 2 months ago
bioconductor-package
13.84 score 1 dependencies 1744 dependentsDeepTarget - 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. We also guided how to interpret the result.
Last updated 2 months ago
bioconductor-package
1.31 score 140 dependenciessurvClust - 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 3 months ago
bioconductor-package
0.09 score 53 dependenciesenhancerHomologSearch -
Last updated 2 years ago
RadioGx -
Last updated 4 years ago