VCF filter rulesUpdated 2 days ago

Kévin Rue-Albrecht

Rendered from VcfFilterRules.Rmd in TVTB 1.31.1.
gDRutilsUpdated 2 days ago

gDR team

Rendered from gDRutils.Rmd in gDRutils 1.3.3.
lute algorithm class definitions and usesUpdated 2 days ago

Sean K. Maden, Stephanie C. Hicks

Rendered from lute_algorithm_classes.Rmd in lute 1.1.0.
The lute user's guideUpdated 2 days ago

Sean K. Maden, Stephanie C. Hicks

Rendered from lute_users_guide.Rmd in lute 1.1.0.
FAERS-PharmacovigilanceUpdated 4 days ago

Yun Peng

Rendered from FAERS-Pharmacovigilance.Rmd in faers 1.1.3.
SparseArray objectsUpdated 5 days ago

Hervé Pagès

Rendered from SparseArray_objects.Rmd in SparseArray 1.5.14.
systemPipeR: Workflow Environment for Data Analysis and Report GenerationUpdated 5 days ago

Author: Le Zhang, Daniela Cassol, and Thomas Girke

Rendered from systemPipeR.Rmd in systemPipeR 2.11.2.
qc-tidyingUpdated 5 days ago

Oliver M. Crook

Rendered from qc-streamlined.Rmd in hdxmsqc 1.1.1.
SGCP package manualUpdated 6 days ago

Niloofar Aghaieabiane

Rendered from SGCP.Rmd in SGCP 1.5.2.
HoloFoodR: interface to HoloFoodR databaseUpdated 8 days ago

Tuomas Borman

Rendered from HoloFoodR.Rmd in HoloFoodR 0.99.8.
Introduction to hermesUpdated 9 days ago

Daniel Sabanés Bové, Namrata Bhatia, Stefanie Bienert, Benoit Falquet, Haocheng Li, Jeff Luong, Lyndsee Midori Zhang, Alex Richardson, Simona Rossomanno, Tim Treis, Mark Yan, Naomi Chang, Chendi Liao, Carolyn Zhang, Joseph N. Paulson

Rendered from hermes.Rmd in hermes 1.9.1.
MatrixQCvis: shiny-based interactive data quality exploration of omics dataUpdated 9 days ago

Thomas Naake and Wolfgang Huber

Rendered from MatrixQCvis.Rmd in MatrixQCvis 1.13.5.
lefser: a Megatanomic biomarker discovery toolUpdated 10 days ago

Asya Khleborodova, Sehyun Oh, Ludwig Geistlinger, and Levi Waldron

Rendered from lefser.Rmd in lefser 1.15.3.
Guided tutorial to COTAN V.2Updated 11 days ago

Silvia Giulia Galfrè

Rendered from Guided_tutorial_v2.Rmd in COTAN 2.5.6.
Cepo for differential stability analysis of scRNA-seq dataUpdated 12 days ago

Hani Jieun Kim

Rendered from cepo.Rmd in Cepo 1.11.2.
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacksUpdated 12 days ago

Ghislain FIEVET [email protected]

Rendered from vign01_adverSCarial.Rmd in adverSCarial 1.3.5.
Introduction_1_loadmetadataUpdated 12 days ago

Hangjia Zhao

Rendered from Introduction_1_loadmetadata.Rmd in pgxRpi 1.1.4.
Using a BioMart other than EnsemblUpdated 12 days ago

Steffen Durinck, Wolfgang Huber, Mike Smith

Rendered from accessing_other_marts.Rmd in biomaRt 2.61.2.
Using the ResidualMatrix classUpdated 15 days ago

Aaron Lun

Rendered from ResidualMatrix.Rmd in ResidualMatrix 1.15.1.
Differential discovery with CATALYSTUpdated 15 days ago

Helena L Crowell, Mark D Robinson

Rendered from differential.Rmd in CATALYST 1.29.1.
Exploring scRNA-seq data from 5 cancer cell lines with scBubbletreeUpdated 15 days ago

Simo Kitanovski ([email protected])

Rendered from User_manual.Rmd in scBubbletree 1.7.16.
EpiDISH - Epigenetic Dissection of Intra-Sample-HeterogeneityUpdated 16 days ago

Shijie C. Zheng, Andrew E. Teschendorff

Rendered from EpiDISH.Rmd in EpiDISH 2.21.1.
BioTIP: an R-package for Characterization of Biological Tipping-PointsUpdated 17 days ago

Zhezhen Wang, Andrew Goldstein, Yuxi Sun, Biniam Feleke, Qier An, Antonio Feliciano, Ieva Tolkaciovaite, and Xinan H Yang

Rendered from BioTIP.Rmd in BioTIP 1.19.0.
mia: Microbiome analysis toolsUpdated 18 days ago

Tuomas Borman

Rendered from mia.Rmd in mia 1.13.23.
CoGAPS - Coordinated Gene Association in Pattern SetsUpdated 18 days ago

Jeanette Johnson, Ashley Tsang, Thomas Sherman, Genevieve Stein-O'Brien, Hyejune Limb, Elana Fertig

Rendered from CoGAPS.Rmd in CoGAPS 3.25.1.
trackViewer Vignette: lollipopPlotUpdated 19 days ago

Jianhong Ou, Lihua Julie Zhu

Rendered from lollipopPlot.Rmd in trackViewer 1.41.3.
Evaluation of Bioinformatics Metrics with evaluomeRUpdated 19 days ago

José Antonio Bernabé-Díaz, Manuel Franco, Juana-María Vivo, Manuel Quesada-Martínez, Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis

Rendered from manual.Rmd in evaluomeR 1.21.6.
Accessing the KEGG REST APIUpdated 19 days ago

Bioconductor Package Maintainer

Rendered from KEGGREST-vignette.Rmd in KEGGREST 1.45.1.
Introduction to SANTAUpdated 19 days ago

Alex Cornish

Rendered from SANTA-vignette.Rmd in SANTA 2.41.2.
Epiregulon tutorial with MultiAssayExperimentUpdated 19 days ago

Xiaosai Yao

Rendered from multiome.mae.Rmd in epiregulon 1.1.2.
Gene Set Analysis in R -- the GSAR PackageUpdated 22 days ago

Yasir Rahmatallah

Rendered from GSAR.Rnw in GSAR 1.39.2.
Introduction_2_loadvariantsUpdated 22 days ago

Hangjia Zhao

Rendered from Introduction_2_loadvariants.Rmd in pgxRpi 1.1.4.
Introduction_3_loadfrequencyUpdated 22 days ago

Hangjia Zhao

Rendered from Introduction_3_loadfrequency.Rmd in pgxRpi 1.1.4.
Introduction_4_process_pgxsegUpdated 22 days ago

Hangjia Zhao

Rendered from Introduction_4_process_pgxseg.Rmd in pgxRpi 1.1.4.
MOSimUpdated 23 days ago

Sonia Tarazona

Rendered from MOSim.Rnw in MOSim 2.1.0.
ENmix User's GuideUpdated 23 days ago

Zongli Xu, Liang Niu, Jack Taylor

Rendered from ENmix.Rmd in ENmix 1.41.2.
statTargetUpdated 24 days ago

Hemi Luan

Rendered from statTarget.Rmd in statTarget 1.35.1.
goseq User's GuideUpdated 24 days ago

Federico Marini

Rendered from goseq.Rnw in goseq 1.57.2.
RI correction extraUpdated 24 days ago

Alvaro Cuadros-Inostroza

Rendered from RICorrection.Rnw in TargetSearch 2.7.1.
The TargetSearch PackageUpdated 24 days ago

Alvaro Cuadros-Inostroza

Rendered from TargetSearch.Rnw in TargetSearch 2.7.1.
Introduction to Clustering of Local Indicators of Spatial Assocation (LISA) curvesUpdated 24 days ago

Nicolas Canete, Ellis Patrick

Rendered from lisaClust.Rmd in lisaClust 1.13.1.
An Introduction to the GenomicRanges PackageUpdated 25 days ago

Marc Carlson, Patrick Aboyoun, Hervé Pagès, and Martin Morgan

Rendered from GenomicRangesIntroduction.Rmd in GenomicRanges 1.57.1.
GenomicRanges HOWTOsUpdated 25 days ago

Hervé Pagès

Rendered from GenomicRangesHOWTOs.Rnw in GenomicRanges 1.57.1.
Introduction to AlpsNMR (older API)Updated 27 days ago

AlpsNMR authors

Rendered from Vig01b-introduction-to-alpsnmr-old-api.Rmd in AlpsNMR 4.7.1.
Introduction to AlpsNMRUpdated 27 days ago

AlpsNMR authors

Rendered from Vig01-introduction-to-alpsnmr.Rmd in AlpsNMR 4.7.1.
Introduction to squallmsUpdated 28 days ago

William Kumler

Rendered from intro_to_squallms.Rmd in squallms 0.99.6.
MultipleAlignment ObjectsUpdated 29 days ago

Marc Carlson, Beryl Kanali

Rendered from MultipleAlignments.Rmd in Biostrings 2.73.1.
autonomics: platform-aware analysisUpdated 29 days ago

Aditya Bhagwat

Rendered from autonomics_platformaware_analysis.Rmd in autonomics 1.13.19.
PIPETSUpdated 30 days ago

Author: Quinlan Furumo

Rendered from PIPETS.Rmd in PIPETS 1.1.1.
scDotPlotUpdated 30 days ago

Ben Laufer

Rendered from scDotPlot.Rmd in scDotPlot 0.99.3.
TENxIO: Import Single Cell Data FilesUpdated 30 days ago

Marcel Ramos

Rendered from TENxIO.Rmd in TENxIO 1.7.1.
Annotation & AlignmentUpdated 1 months ago

Haakon Tjeldnes & Kornel Labun

Rendered from Annotation_Alignment.Rmd in ORFik 1.25.3.
Data managementUpdated 1 months ago

Haakon Tjeldnes & Kornel Labun

Rendered from ORFikExperiment.Rmd in ORFik 1.25.3.
ORFik OverviewUpdated 1 months ago

Haakon Tjeldnes & Kornel Labun

Rendered from ORFikOverview.Rmd in ORFik 1.25.3.
Package DetailsUpdated 1 months ago

Christian Arnold

Rendered from GRaNIE_packageDetails.Rmd in GRaNIE 1.9.1.
GRaNIE single-cell eGRN inferenceUpdated 1 months ago

Christian Arnold

Rendered from GRaNIE_singleCell_eGRNs.Rmd in GRaNIE 1.9.1.
Using broadSeq to analyze RNA-seq dataUpdated 1 months ago

Rishi Das Roy

Rendered from broadSeq.Rmd in broadSeq 0.99.3.
IntroductionUpdated 1 months ago

Dany Mukesha

Rendered from Introduction.Rmd in BioGA 0.99.6.
Quickstart Guide to ggseqalignUpdated 1 months ago

Simeon Lim Rossmann

Rendered from ggseqalign.Rmd in ggseqalign 0.99.1.
PhyloProfileUpdated 1 months ago

Vinh Tran

Rendered from PhyloProfile-vignette.Rmd in PhyloProfile 1.19.4.
cbaf: an automated, easy-to-use R package for comparing omic data across multiple cancers / a cancer's subgroupsUpdated 1 months ago

Arman Shahrisa

Rendered from cbaf.Rmd in cbaf 1.27.4.
Detecting Obscure Tandem Repeats in SequencesUpdated 1 months ago

Erik Wright

Rendered from RepeatRepeat.Rnw in DECIPHER 3.1.4.
dream analysisUpdated 1 months ago

Developed by Gabriel Hoffman

Rendered from dream.Rmd in variancePartition 1.35.4.
STRINGdb VignetteUpdated 1 months ago

Damian Szklarczyk

Rendered from STRINGdb.Rnw in STRINGdb 2.17.3.
Computing RNA velocity in a Bioconductor frameworkUpdated 1 months ago

Kevin Rue-Albrecht, Aaron Lun, Charlotte Soneson

Rendered from velociraptor.Rmd in velociraptor 1.15.4.
Analyze and visualize RNA-Seq data with pathlinkRUpdated 1 months ago

Andy An, Travis Blimkie

Rendered from pathlinkR.Rmd in pathlinkR 1.1.12.
Creating CompoundDb annotation resourcesUpdated 1 months ago

Johannes Rainer

Rendered from create-compounddb.Rmd in CompoundDb 1.9.1.
Usage of Annotation Resources with the CompoundDb PackageUpdated 1 months ago

Johannes Rainer

Rendered from CompoundDb-usage.Rmd in CompoundDb 1.9.1.
CAGEr: an R package for CAGE (Cap Analysis of Gene Expression) data analysis and promoterome miningUpdated 1 months ago

Vanja Haberle, Charles Plessy, Sarvesh Nikumbh

Rendered from CAGEexp.Rmd in CAGEr 2.11.3.
Basic usage of GBScleanRUpdated 1 months ago

Tomoyuki Furuta, Institute of Plant Science and Resources, Okayama University, Okayama, Japan, [email protected]

Rendered from BasicUsageOfGBScleanR.rmd in GBScleanR 1.9.20.
VariantExperiment: A RangedSummarizedExperiment Container for Large-Scale Variant Data with GDS BackendUpdated 1 months ago

Qian Liu

Rendered from VariantExperiment-class.Rmd in VariantExperiment 1.19.2.
GDSArray: Representing GDS files as array-like objectsUpdated 1 months ago

Qian Liu, Hervé Pagès, Martin Morgan

Rendered from GDSArray.Rmd in GDSArray 1.25.2.
Description and usage of Spectra objectsUpdated 2 months ago

RforMassSpectrometry Package Maintainer

Rendered from Spectra.Rmd in Spectra 1.15.3.
gDRimportUpdated 2 months ago

gDR team

Rendered from gDRimport.Rmd in gDRimport 1.3.2.
Introduction to BatchQCUpdated 2 months ago

W. Evan Johnson, Jessica McClintock

Rendered from BatchQC_Intro.Rmd in BatchQC 2.1.2.
recount quick start guideUpdated 2 months ago

Leonardo Collado-Torres

Rendered from recount-quickstart.Rmd in recount 1.31.2.
trackViewer Vignette: plot interaction dataUpdated 2 months ago

Jianhong Ou, Lihua Julie Zhu

Rendered from plotInteractionData.Rmd in trackViewer 1.41.3.
Segmenting and normalizing multiplexed imaging data with simpleSegUpdated 2 months ago

Alexander Nicholls, Ellis Patrick, Nicolas Canete

Rendered from simpleSeg.Rmd in simpleSeg 1.7.1.
Getting Started DECIPHERingUpdated 2 months ago

Erik Wright

Rendered from DECIPHERing.Rnw in DECIPHER 3.1.4.
Searching biological sequencesUpdated 2 months ago

Erik Wright

Rendered from SearchForResearch.Rnw in DECIPHER 3.1.4.
Spatial Mixed-Effects Modelling with spicyUpdated 2 months ago

Nicolas Canete, Ellis Patrick

Rendered from spicyR.Rmd in spicyR 1.17.1.
Performing meta-analyses of microbiome studies with MMUPHinUpdated 2 months ago

Siyuan Ma

Rendered from MMUPHin.Rmd in MMUPHin 1.19.1.
The seqsetvis packageUpdated 2 months ago

Joseph R Boyd

Rendered from seqsetvis_overview.Rmd in seqsetvis 1.25.2.
missMethyl: Analysing Illumina HumanMethylation BeadChip DataUpdated 2 months ago

Belinda Phipson and Jovana Maksimovic

Rendered from missMethyl.Rmd in missMethyl 1.39.13.
Use of CAGE resources with CAGErUpdated 2 months ago

Vanja Haberle, Charles Plessy

Rendered from CAGE_Resources.Rmd in CAGEr 2.11.3.
Working with large arrays in R (slides from July 2017)Updated 2 months ago

Hervé Pagès

Rendered from A-Working_with_large_arrays.Rnw in DelayedArray 0.31.5.
Implementing A DelayedArray BackendUpdated 2 months ago

Hervé Pagès

Rendered from B-Implementing_a_backend.Rmd in DelayedArray 0.31.5.
A DelayedArray / HDF5Array update (slides from April 2021)Updated 2 months ago

Hervé Pagès

Rendered from C-DelayedArray_HDF5Array_update.Rnw in DelayedArray 0.31.5.
Cardinal 3: User guide for mass spectrometry imaging analysisUpdated 2 months ago

Kylie Ariel Bemis

Rendered from Cardinal3-guide.Rmd in Cardinal 3.7.1.
Design Group-Specific FISH ProbesUpdated 2 months ago

Erik Wright

Rendered from DesignProbes.Rnw in DECIPHER 3.1.4.
The Art of Multiple Sequence Alignment in RUpdated 2 months ago

Erik Wright

Rendered from ArtOfAlignmentInR.Rnw in DECIPHER 3.1.4.
PiratUpdated 2 months ago

Lucas Etourneau, Samuel Wieczorek"

Rendered from Pirat.Rmd in Pirat 0.99.26.
Fast functional enrichmentUpdated 2 months ago

Marek Gierlinski

Rendered from fenr.Rmd in fenr 1.3.1.
Cardinal 3: Statistical methods for mass spectrometry imagingUpdated 2 months ago

Kylie Ariel Bemis

Rendered from Cardinal3-stats.Rmd in Cardinal 3.7.1.
gDR annotationUpdated 2 months ago

gDR team

Rendered from gDR-annotation.Rmd in gDRcore 1.3.2.
Definition of binding sites from iCLIP signalUpdated 2 months ago

Mirko Brüggemann, Kathi Zarnack

Rendered from vignette.Rmd in BindingSiteFinder 2.3.1.
Biostrings Quick OverviewUpdated 2 months ago

Hervé Pagès

Rendered from BiostringsQuickOverview.Rnw in Biostrings 2.73.1.
Pairwise Sequence AlignmentsUpdated 2 months ago

Hervé Pagès

Rendered from PairwiseAlignments.Rnw in Biostrings 2.73.1.
IntroductionUpdated 3 months ago

Constantin Ahlmann-Eltze

Rendered from Introduction.Rmd in lemur 1.3.2.
Growing Phylogenetic Trees with TreeLineUpdated 3 months ago

Erik Wright

Rendered from GrowingTrees.Rnw in DECIPHER 3.1.4.
Upsize Your Clustering with ClusterizeUpdated 3 months ago

Erik Wright

Rendered from ClusteringSequences.Rnw in DECIPHER 3.1.4.
BiocCheck: Ensuring Bioconductor package guidelinesUpdated 3 months ago

Marcel Ramos

Rendered from BiocCheck.Rmd in BiocCheck 1.41.3.
miaVizUpdated 3 months ago

Tuomas Borman

Rendered from miaViz.Rmd in miaViz 1.13.2.
Gene set variation analysisUpdated 3 months ago

Robert Castelo, Axel Klenk, Justin Guinney

Rendered from GSVA.Rmd in GSVA 1.53.3.
Simulating Single-Cell Multi-Omics Data with MOSimUpdated 3 months ago

Carolina Monzó, Ángeles Arzalluz-Luque, Arianna Febbo, Sonia Tarazona

Rendered from scMOSim.Rmd in MOSim 2.1.0.
A quick overview of the S4Arrays packageUpdated 3 months ago

Hervé Pagès

Rendered from S4Arrays_quick_overview.Rmd in S4Arrays 1.5.3.
The GeDi User's GuideUpdated 3 months ago

Annekathrin Silvia Nedwed, Federico Marini

Rendered from GeDi_manual.Rmd in GeDi 1.1.1.
BatchQC ExamplesUpdated 3 months ago

W. Evan Johnson, Jessica McClintock, Solaiappan Manimaran

Rendered from BatchQC_examples.Rmd in BatchQC 2.1.2.
Quantitative features for mass spectrometry dataUpdated 3 months ago

Laurent Gatto

Rendered from QFeatures.Rmd in QFeatures 1.15.2.
An Overview of the S4Vectors packageUpdated 3 months ago

Patrick Aboyoun, Michael Lawrence, Hervé Pagès

Rendered from S4VectorsOverview.Rmd in S4Vectors 0.43.1.
Making TxDb ObjectsUpdated 3 months ago

Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon, Martin Morgan

Rendered from txdbmaker.Rmd in txdbmaker 1.1.1.
Data visualization from a QFeatures objectUpdated 3 months ago

Laurent Gatto

Rendered from Visualization.Rmd in QFeatures 1.15.2.
Processing quantitative proteomics data with QFeaturesUpdated 3 months ago

Laurent Gatto

Rendered from Processing.Rmd in QFeatures 1.15.2.
How to use iSEE with big dataUpdated 3 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from bigdata.Rmd in iSEE 2.17.1.
Controlling the iSEE interface using speech recognitionUpdated 3 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from voice.Rmd in iSEE 2.17.1.
An introduction to the MoleculeExperiment ClassUpdated 3 months ago

Bárbara Zita Peters Couto, Nick Robertson, Mu-Wei Chung, Ellis Patrick, Shila Ghazanfar

Rendered from MoleculeExperiment.Rmd in MoleculeExperiment 1.5.1.
Interacting with the gypsum REST APIUpdated 3 months ago

Aaron Lun

Rendered from userguide.Rmd in gypsum 1.1.6.
Preprocessing with CATALYSTUpdated 3 months ago

Helena L Crowell, Vito RT Zanotelli, Stéphane Chevrier, Bernd Bodenmiller, Mark D Robinson

Rendered from preprocessing.Rmd in CATALYST 1.29.1.
OverviewUpdated 3 months ago

William Hutchison, Stefano Mangiola

Rendered from overview.Rmd in tidySpatialExperiment 1.1.1.
A quick start guide to smartid: Scoring and MARker selection method based on modified Tf-IDfUpdated 3 months ago

Jinjin Chen

Rendered from smartid_Demo.Rmd in smartid 1.1.2.
The simona packageUpdated 3 months ago

Zuguang Gu ([email protected])

Rendered from simona.Rmd in simona 1.3.1.
Building protein networks around drug-targets using OmnipathRUpdated 4 months ago

Attila Gabor, Alberto Valdeolivas, Julio Saez-Rodriguez

Rendered from drug_targets.Rmd in OmnipathR 3.13.1.
OmnipathR: an R client for the OmniPath web serviceUpdated 4 months ago

Alberto Valdeolivas, Attila Gabor, Denes Turei, Julio Saez-Rodriguez

Rendered from omnipath_intro.Rmd in OmnipathR 3.13.1.
ginmappeRUpdated 4 months ago

Fernando Sola, Daniel Ayala, Marina Pulido, Rafael Ayala, Lorena López-Cerero, Inma Hernández, David Ruiz

Rendered from ginmappeR.Rmd in ginmappeR 1.1.2.
Pseudobulk cell size rescaling exampleUpdated 4 months ago

Sean K. Maden

Rendered from lute_pseudobulk_example.Rmd in lute 1.1.0.
Tximeta: transcript quantification import with automatic metadataUpdated 4 months ago

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Rob Patro

Rendered from tximeta.Rmd in tximeta 1.23.2.
spillR VignetteUpdated 4 months ago

Marco Guazzini, Alexander G. Reisach, Sebastian Weichwald, Christof Seiler

Rendered from spillR-vignette.Rmd in spillR 1.1.1.
scRNAseqApp GuideUpdated 4 months ago

Jianhong Ou

Rendered from scRNAseqApp.Rmd in scRNAseqApp 1.5.7.
Converting PharmacoSet Drug Response Data into gDR objectUpdated 4 months ago

Jermiah Joseph, Bartosz Czech

Rendered from ConvertingPharmacoSetToGDR.Rmd in gDRimport 1.3.2.
An introduction to QuasRUpdated 4 months ago

Michael Stadler, Dimos Gaidatzis, Charlotte Soneson, Anita Lerch

Rendered from QuasR.Rmd in QuasR 1.45.1.
gDRcoreUpdated 4 months ago

gDR team

Rendered from gDRcore.Rmd in gDRcore 1.3.2.
Motif Analysis Using motifTestRUpdated 4 months ago

Stevie Pederson

Rendered from motifAnalysis.Rmd in motifTestR 1.1.3.
Creating new MsBackend classesUpdated 4 months ago

RforMassSpectrometry Package Maintainer

Rendered from MsBackend.Rmd in Spectra 1.15.3.
Large-scale data handling and processing with SpectraUpdated 4 months ago

RforMassSpectrometry Package Maintainer

Rendered from Spectra-large-scale.Rmd in Spectra 1.15.3.
Saving objects to artifacts and back againUpdated 4 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.base 1.5.3.
Other single-cell RNA-seq analysis utilitiesUpdated 4 months ago

Aaron Lun

Rendered from misc.Rmd in scuttle 1.15.1.
Using gDRstyleUpdated 4 months ago

gDR team

Rendered from gDRstyle.Rmd in gDRstyle 1.3.2.
Automation and Visualization of Flow Cytometry Data Analysis PipelinesUpdated 4 months ago

Philippe Hauchamps, Laurent Gatto

Rendered from CytoPipeline.Rmd in CytoPipeline 1.5.1.
Converting a gDR-generated MultiAssayExperiment object into a PharmacoSetUpdated 5 months ago

Jermiah Joseph, Bartosz Czech

Rendered from ConvertingMAEtoPharmacoSet.Rmd in gDRimport 1.3.2.
trackViewer Vignette: change the track stylesUpdated 5 months ago

Jianhong Ou, Lihua Julie Zhu

Rendered from changeTracksStyles.Rmd in trackViewer 1.41.3.
Using SingleR to annotate single-cell RNA-seq dataUpdated 5 months ago

Aaron Lun, Jared M. Andrews, Friederike Dündar, Daniel Bunis

Rendered from SingleR.Rmd in SingleR 2.7.1.
spoon TutorialUpdated 5 months ago

Kinnary H. Shah, Boyi Guo, Stephanie C. Hicks

Rendered from spoon.Rmd in spoon 1.1.3.
Introduction to the AnVIL packageUpdated 5 months ago

Nitesh Turaga, Vincent Carey, BJ Stubbs, Marcel Ramos, Martin Morgan

Rendered from Introduction.Rmd in AnVIL 1.17.6.
gDR style guideUpdated 5 months ago

gDR team

Rendered from style_guide.Rmd in gDRstyle 1.3.2.
Using oligonucleotide microarray reporter sequence information for preprocessing and quality assessmentUpdated 5 months ago

Wolfgang Huber, Robert Gentleman

Rendered from matchprobes.Rmd in Biostrings 2.73.1.
Design Group-Specific PrimersUpdated 5 months ago

Erik Wright

Rendered from DesignPrimers.Rnw in DECIPHER 3.1.4.
Design Microarray ProbesUpdated 5 months ago

Erik Wright

Rendered from DesignMicroarray.Rnw in DECIPHER 3.1.4.
Design Primers That Yield Group-Specific SignaturesUpdated 5 months ago

Erik Wright

Rendered from DesignSignatures.Rnw in DECIPHER 3.1.4.
Finding Chimeric SequencesUpdated 5 months ago

Erik Wright

Rendered from FindChimeras.Rnw in DECIPHER 3.1.4.
trackViewer Vignette: overviewUpdated 5 months ago

Jianhong Ou, Lihua Julie Zhu

Rendered from trackViewer.Rmd in trackViewer 1.41.3.
gDR -- data modelUpdated 5 months ago

gDR team

Rendered from gDR-data-model.Rmd in gDRcore 1.3.2.
ggkeggUpdated 5 months ago

Noriaki Sato

Rendered from usage_of_ggkegg.Rmd in ggkegg 1.3.2.
MultiAssayExperiment: The Integrative Bioconductor ContainerUpdated 5 months ago

MultiAssay Special Interest Group

Rendered from MultiAssayExperiment.Rmd in MultiAssayExperiment 1.31.3.
BiocSklearn -- exposing python Scikit machine learning elements for BioconductorUpdated 5 months ago

Vincent J. Carey, stvjc at channing.harvard.edu, Shweta Gopaulakrishnan, reshg at channing.harvard.edu, Samuela Pollack, spollack at jimmy.harvard.edu

Rendered from BiocSklearn.Rmd in BiocSklearn 1.27.1.
Error handlingUpdated 5 months ago

Developed by Gabriel Hoffman

Rendered from errors.Rmd in dreamlet 1.3.1.
ChIPpeakAnno: annotate, visualize, and compare peak dataUpdated 5 months ago

Jianhong Ou, Kai Hu, Haibo Liu, Junhui Li, Jun Yu, Lihua Julie Zhu

Rendered from ChIPpeakAnno.Rmd in ChIPpeakAnno 3.39.1.
Accessing Ensembl annotation with biomaRtUpdated 5 months ago

Mike L. Smith, Steffen Durinck, Wolfgang Huber

Rendered from accessing_ensembl.Rmd in biomaRt 2.61.2.
gDR suiteUpdated 6 months ago

gDR team

Rendered from gDR.Rmd in gDR 1.3.1.
Dreamlet analysis of single cell RNA-seqUpdated 6 months ago

Developed by Gabriel Hoffman

Rendered from dreamlet.Rmd in dreamlet 1.3.1.
The Magic of Gene FindingUpdated 6 months ago

Erik Wright

Rendered from FindingGenes.Rnw in DECIPHER 3.1.4.
scDblFinderUpdated 6 months ago

Pierre-Luc Germain

Rendered from scDblFinder.Rmd in scDblFinder 1.19.1.
Overview of BiocPkgToolsUpdated 6 months ago

Shian Su, Vince Carey, Marcel Ramos, Lori Shepherd, Martin Morgan, Sean Davis

Rendered from BiocPkgTools.Rmd in BiocPkgTools 1.23.1.
GenomicPlot: an R package for efficient and flexible visualization of genome-wide NGS coverage profilesUpdated 6 months ago

Shuye Pu

Rendered from GenomicPlot_vignettes.rmd in GenomicPlot 1.3.3.
SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of InterestUpdated 6 months ago

Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

Rendered from SummarizedExperiment.Rmd in SummarizedExperiment 1.35.1.
Save/load spatial omics data to/from fileUpdated 6 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.spatial 1.5.1.
Running an AnVIL workflow within RUpdated 7 months ago

Kayla Interdonato, Yubo Cheng, Martin Morgan

Rendered from RunningWorkflow.Rmd in AnVIL 1.17.6.
Saving SingleCellExperiments to artifacts and back againUpdated 7 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.sce 1.5.1.
Saving SummarizedExperiments to artifacts and back againUpdated 7 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.se 1.5.2.
Saving arrays to artifacts and back againUpdated 7 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.matrix 1.5.4.
An introduction to the iSEE interfaceUpdated 7 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from basic.Rmd in iSEE 2.17.1.
Sharing information across iSEE panelsUpdated 7 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from links.Rmd in iSEE 2.17.1.
Configuring iSEE appsUpdated 7 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from configure.Rmd in iSEE 2.17.1.
Describing the ExperimentColorMap classUpdated 7 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from ecm.Rmd in iSEE 2.17.1.
Deploying custom panels in the iSEE interfaceUpdated 7 months ago

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered from custom.Rmd in iSEE 2.17.1.
Macarron User ManualUpdated 7 months ago

Amrisha Bhosle, Ludwig Geistlinger, Sagun Maharjan

Rendered from Macarron.Rmd in Macarron 1.9.1.
IsoBayesUpdated 8 months ago

Jordy Bollon, Simone Tiberi

Rendered from IsoBayes.Rmd in IsoBayes 1.3.2.
Saving genomic ranges to artifacts and back againUpdated 8 months ago

Aaron Lun

Rendered from userguide.Rmd in alabaster.ranges 1.5.2.
Getting Started with ClassifyRUpdated 8 months ago

Dario Strbenac, Ellis Patrick, Graham Mann, Jean Yang, John Ormerod <br> The University of Sydney, Australia.

Rendered from ClassifyR.Rmd in ClassifyR 3.9.2.
Quantifying cell colocalisation with SPIATUpdated 8 months ago

Yuzhou Feng

Rendered from cell-colocalisation.Rmd in SPIAT 1.7.1.
Modeling continuous cell-level covariatesUpdated 8 months ago

Developed by Gabriel Hoffman

Rendered from cell_covs.Rmd in dreamlet 1.3.1.
GRaNIE Workflow ExampleUpdated 8 months ago

Christian Arnold

Rendered from GRaNIE_workflow.Rmd in GRaNIE 1.9.1.
Differential Allelic Representation (DAR) analysisUpdated 9 months ago

Lachlan Baer, Stevie Pederson

Rendered from dar.Rmd in tadar 1.3.1.
Overview of DelayedMatrixStatsUpdated 9 months ago

Peter Hickey

Rendered from DelayedMatrixStatsOverview.Rmd in DelayedMatrixStats 1.27.1.
cytoviewer - Interactive multi-channel image visualization in RUpdated 9 months ago

Lasse Meyer, Nils Eling

Rendered from cytoviewer.Rmd in cytoviewer 1.5.0.
Classify SequencesUpdated 9 months ago

Erik Wright

Rendered from ClassifySequences.Rnw in DECIPHER 3.1.4.
The Double Life of RNA: Uncovering Non-Coding RNAsUpdated 9 months ago

Erik Wright

Rendered from FindingNonCodingRNAs.Rnw in DECIPHER 3.1.4.
Example using structToolboxUpdated 10 months ago

Gavin R Lloyd, Ralf J Weber

Rendered from example_using_structToolbox.Rmd in metabolomicsWorkbenchR 1.15.2.
Introduction to metabolomicsWorkbenchRUpdated 10 months ago

Gavin R Lloyd, Ralf J Weber

Rendered from Introduction_to_metabolomicsWorkbenchR.Rmd in metabolomicsWorkbenchR 1.15.2.
sechmUpdated 10 months ago

Pierre-Luc Germain

Rendered from sechm.Rmd in sechm 1.13.1.
A quick start guide to the hoodscanR packageUpdated 10 months ago

Ning Liu, Melissa Davis

Rendered from Quick_start.Rmd in hoodscanR 1.3.1.
Error handlingUpdated 10 months ago

Developed by Gabriel Hoffman

Rendered from errors.Rmd in variancePartition 1.35.4.
Frequently asked questionsUpdated 10 months ago

Developed by Gabriel Hoffman

Rendered from FAQ.Rmd in variancePartition 1.35.4.
Multivariate testsUpdated 10 months ago

Developed by Gabriel Hoffman

Rendered from mvtests.Rmd in variancePartition 1.35.4.
The wateRmelon User's GuideUpdated 10 months ago

Tyler Gorrie-Stone, Leonard Schalkwyk

Rendered from wateRmelon.Rmd in wateRmelon 2.11.2.
Vign02_overView_analysisUpdated 10 months ago

Ghislain FIEVET

Rendered from vign02_overView_analysis.Rmd in adverSCarial 1.3.5.
Vign03_adaptClassifierUpdated 10 months ago

Ghislain FIEVET

Rendered from vign03_adapt_classifier.Rmd in adverSCarial 1.3.5.
Vign04_advRandWalkMinChangeUpdated 10 months ago

Ghislain FIEVET

Rendered from vign04_advRandWalkMinChange.Rmd in adverSCarial 1.3.5.
Testing non-linear effectsUpdated 11 months ago

Developed by Gabriel Hoffman

Rendered from non_lin_eff.Rmd in dreamlet 1.3.1.
Variance partitioning analysisUpdated 11 months ago

Developed by Gabriel Hoffman

Rendered from variancePartition.Rmd in variancePartition 1.35.4.
Additional visualizations of variance structureUpdated 11 months ago

Developed by Gabriel Hoffman

Rendered from additional_visualization.Rmd in variancePartition 1.35.4.
Theory and practice of random effectsUpdated 11 months ago

Developed by Gabriel Hoffman

Rendered from rnd_effects.Rmd in variancePartition 1.35.4.
CardinalIO: Parsing and writing imzML filesUpdated 11 months ago

Kylie Ariel Bemis

Rendered from CardinalIO-guide.Rmd in CardinalIO 1.3.1.
mashr analysis after dreamletUpdated 11 months ago

Developed by Gabriel Hoffman

Rendered from mashr.Rmd in dreamlet 1.3.1.
Handling large H5AD datasetsUpdated 11 months ago

Developed by Gabriel Hoffman

Rendered from h5ad_on_disk.Rmd in dreamlet 1.3.1.
Working with transcriptsUpdated 11 months ago

Haakon Tjeldnes & Kornel Labun

Rendered from Working_with_transcripts.Rmd in ORFik 1.25.3.
Matter 2: User guide for flexible out-of-memory data structuresUpdated 11 months ago

Kylie Ariel Bemis

Rendered from matter-2-guide.Rmd in matter 2.7.2.
On Using and Extending the MsBackendRawFileReader BackendUpdated 12 months ago

Tobias Kockmann, Christian Panse

Rendered from MsBackendRawFileReader.Rmd in MsBackendRawFileReader 1.11.3.
Doublet identifiation in single-cell ATAC-seqUpdated 12 months ago

Pierre-Luc Germain

Rendered from scATAC.Rmd in scDblFinder 1.19.1.
Developing packages with beachmatUpdated 1 years ago

Aaron Lun

Rendered from linking.Rmd in beachmat 2.21.3.
Demonstration of the CytoPipeline R package suite functionalitiesUpdated 1 years ago

Philippe Hauchamps, Laurent Gatto

Rendered from Demo.Rmd in CytoPipeline 1.5.1.
limma User's GuideUpdated 1 years ago

Gordon Smyth

Rendered from usersguide.Rnw in limma 3.61.2.
A brief introduction to limmaUpdated 1 years ago

Gordon Smyth

Rendered from intro.Rmd in limma 3.61.2.
Using HDF5-backed matrices with beachmatUpdated 1 years ago

Aaron Lun

Rendered from userguide.Rmd in beachmat.hdf5 1.3.1.
Importing dataUpdated 1 years ago

Haakon Tjeldnes & Kornel Labun

Rendered from Importing_Data.Rmd in ORFik 1.25.3.
MSstatsShiny Launch InstructionsUpdated 1 years ago

Devon Kohler ([email protected])

Rendered from MSstatsShiny_Launch_Instructions.Rmd in MSstatsShiny 1.7.2.
Guide to ggmanh PackageUpdated 1 years ago

John Lee

Rendered from ggmanh.Rmd in ggmanh 1.9.7.
Authoring R Markdown vignettesUpdated 1 years ago

Andrzej Oleś, Wolfgang Huber, Martin Morgan

Rendered from AuthoringRmdVignettes.Rmd in BiocStyle 2.33.1.
Combine LC-MS Metabolomics Datasets with metabCombinerUpdated 1 years ago

Hani Habra

Rendered from metabCombiner_vignette.Rmd in metabCombiner 1.15.2.
SpotClean adjusts for spot swapping in spatial transcriptomics dataUpdated 1 years ago

Zijian Ni and Christina Kendziorski

Rendered from SpotClean.Rmd in SpotClean 1.7.1.
Pathway constructionUpdated 1 years ago

Denes Turei

Rendered from paths.Rmd in OmnipathR 3.13.1.
A quick start guide to the standR packageUpdated 1 years ago

Ning Liu, Dharmesh Bhuva, Ahmed Mohamed, Chin Wee Tan, Melissa Davis

Rendered from Quick_start.Rmd in standR 1.9.0.
Ribo-seq pipelineUpdated 1 years ago

Haakon Tjeldnes & Kornel Labun

Rendered from Ribo-seq_pipeline.Rmd in ORFik 1.25.3.
The Netboost users guideUpdated 1 years ago

Pascal Schlosser, Jochen Knaus

Rendered from netboost.Rmd in netboost 2.13.1.
Pseudobulk and differential expressionUpdated 1 years ago

Constantin Ahlmann-Eltze

Rendered from pseudobulk.Rmd in glmGamPoi 1.17.3.
A transfer learning algorithm for spatial proteomicsUpdated 1 years ago

Lisa M. Breckels, Laurent Gatto

Rendered from v05-pRoloc-transfer-learning.Rmd in pRoloc 1.45.1.
Introduction to the scDblFinder packageUpdated 1 years ago

Pierre-Luc Germain, Aaron Lun

Rendered from introduction.Rmd in scDblFinder 1.19.1.
Comprehensive DNA Methylation Analysis with RnBeadsUpdated 2 years ago

Fabian Mueller

Rendered from RnBeads.Rnw in RnBeads 2.23.0.
Submitting your organism to GenomeInfoDbUpdated 2 years ago

Sonali Arora, H. Khan

Rendered from Accept-organism-for-GenomeInfoDb.Rmd in GenomeInfoDb 1.41.1.
immunoClust packageUpdated 2 years ago

Till Soerensen

Rendered from immunoClust.Rnw in immunoClust 1.37.3.
Ten Things You Didn't Know (slides from BioC 2016)Updated 2 years ago

Hervé Pagès

Rendered from Ten_things_slides.Rnw in GenomicRanges 1.57.1.
Rle Tips and TricksUpdated 2 years ago

Patrick Aboyoun, Beryl Kanali

Rendered from RleTricks.Rmd in S4Vectors 0.43.1.
Basic analyses with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from basic_analysis.Rmd in SPIAT 1.7.1.
Characterising tissue structure with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from tissue-structure.Rmd in SPIAT 1.7.1.
Identifying cellular neighborhood with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from neighborhood.Rmd in SPIAT 1.7.1.
Overview of the SPIAT packageUpdated 2 years ago

Anna Trigos, Yuzhou Feng, Tianpei Yang, Mabel Li, John Zhu, Volkan Ozcoban, Maria Doyle

Rendered from SPIAT.Rmd in SPIAT 1.7.1.
Quality control and visualisation with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from quality-control_visualisation.Rmd in SPIAT 1.7.1.
Reading in data and data formatting in SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from data_reading-formatting.Rmd in SPIAT 1.7.1.
Spatial heterogeneity with SPIATUpdated 2 years ago

Yuzhou Feng

Rendered from spatial-heterogeneity.Rmd in SPIAT 1.7.1.
Introduction to the SpatialExperiment classUpdated 2 years ago

Dario Righelli, Helena L. Crowell, Lukas M. Weber

Rendered from SpatialExperiment.Rmd in SpatialExperiment 1.15.1.
ClassifyR Developer's GuideUpdated 2 years ago

Dario Strbenac, Ellis Patrick<br> The University of Sydney, Australia.

Rendered from DevelopersGuide.Rmd in ClassifyR 3.9.2.
The database manager in OmnipathRUpdated 2 years ago

Denes Turei

Rendered from db_manager.Rmd in OmnipathR 3.13.1.
PRAM: Pooling RNA-seq and Assembling ModelsUpdated 2 years ago

Peng Liu, Colin N. Dewey, and Sündüz Keleş

Rendered from pram.Rmd in pram 1.21.1.
Using scifer to filter single-cell sorted B cell receptor (BCR) sanger sequencesUpdated 2 years ago

Rodrigo Arcoverde Cerveira

Rendered from scifer_walkthrough.Rmd in scifer 1.7.3.
Introduction to plotgardenerUpdated 2 years ago

Nicole Kramer, Eric S. Davis, Craig Wenger, Sarah Parker, Erika Deoudes, Michael Love, Douglas H. Phanstiel

Rendered from introduction_to_plotgardener.Rmd in plotgardener 1.11.3.
Handling metadata and annotationsUpdated 2 years ago

AlpsNMR authors

Rendered from Vig02-handling-metadata-and-annotations.Rmd in AlpsNMR 4.7.1.
QC and downstream analysis for differential expression RNA-seqUpdated 2 years ago

Lorena Pantano

Rendered from DEGreport.Rmd in DEGreport 1.41.1.
Introduction to MfuzzUpdated 2 years ago

Matthias Futschik

Rendered from Mfuzz.Rnw in Mfuzz 2.65.0.
Package Quick Start GuideUpdated 2 years ago

Jiefei Wang

Rendered from quick_start_guide.Rmd in SharedObject 1.19.1.
MultiAssayExperiment: Quick Start GuideUpdated 2 years ago

Marcel Ramos & Levi Waldron

Rendered from QuickStartMultiAssay.Rmd in MultiAssayExperiment 1.31.3.
systemPipeR: Workflows collectionUpdated 2 years ago

Author: Daniela Cassol ([email protected]) and Thomas Girke ([email protected])

Rendered from systemPipeR_workflows.Rmd in systemPipeR 2.11.2.
Converting single-cell data structures between Bioconductor and PythonUpdated 2 years ago

Luke Zappia, Aaron Lun

Rendered from zellkonverter.Rmd in zellkonverter 1.15.1.
Interactive and explorative visualization of ExpressionSet using omicsViewerUpdated 2 years ago

Chen Meng

Rendered from quickStart.rmd in omicsViewer 1.9.2.
Data analysis of metabolomics and other omics datasets using the structToolboxUpdated 2 years ago

Gavin R Lloyd, Andris Jankevics, Ralf J Weber

Rendered from data_analysis_omics_using_the_structtoolbox.Rmd in structToolbox 1.17.3.
Single-cell analysis toolkit for expression in RUpdated 2 years ago

Davis McCarthy, Aaron Lun

Rendered from overview.Rmd in scater 1.33.2.
MSstatsTMT : A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labelingUpdated 2 years ago

Ting Huang ([email protected]), Meena Choi ([email protected]), Mateusz Staniak ([email protected]), Sicheng Hao ([email protected]), Olga Vitek([email protected])

Rendered from MSstatsTMT.Rmd in MSstatsTMT 2.13.1.
Resource specific interaction attributesUpdated 2 years ago

Denes Turei

Rendered from extra_attrs.Rmd in OmnipathR 3.13.1.
monaLisa - MOtif aNAlysis with LisaUpdated 2 years ago

Dania Machlab, Lukas Burger, Charlotte Soneson, Michael Stadler

Rendered from monaLisa.Rmd in monaLisa 1.11.1.
OmniPath Bioconductor workshopUpdated 2 years ago

Denes Turei, Alberto Valdeolivas, Attila Gabor, Julio Saez-Rodriguez

Rendered from bioc_workshop.Rmd in OmnipathR 3.13.1.
Using DelayedMatrix with MultiAssayExperimentUpdated 3 years ago

MultiAssay Special Interest Group

Rendered from UsingHDF5Array.Rmd in MultiAssayExperiment 1.31.3.
Pigengene: Computing and using eigengenesUpdated 3 years ago

Habil Zare

Rendered from Pigengene_inference.Rnw in Pigengene 1.31.2.
padma package: Quick-start guideUpdated 3 years ago

Andrea Rau

Rendered from padma.Rmd in padma 1.15.1.
Recovering intra-sample doubletsUpdated 3 years ago

Aaron Lun

Rendered from recoverDoublets.Rmd in scDblFinder 1.19.1.
Using NicheNet with OmnipathRUpdated 3 years ago

Denes Turei, Alberto Valdeolivas, Julio Saez-Rodriguez

Rendered from nichenet.Rmd in OmnipathR 3.13.1.
RnBeads AnnotationUpdated 3 years ago

Fabian Mueller

Rendered from RnBeads_Annotations.Rnw in RnBeads 2.23.0.
Effect size estimation with apeglmUpdated 3 years ago

Anqi Zhu, Joseph G. Ibrahim, and Michael I. Love

Rendered from apeglm.Rmd in apeglm 1.27.1.
Detecting clusters of doublet cells with DE analysesUpdated 3 years ago

Aaron Lun

Rendered from findDoubletClusters.Rmd in scDblFinder 1.19.1.
Scoring potential doublets from simulated densitiesUpdated 3 years ago

Aaron Lun

Rendered from computeDoubletDensity.Rmd in scDblFinder 1.19.1.
trackViewer Vignette: dandelionPlotUpdated 3 years ago

Jianhong Ou, Lihua Julie Zhu

Rendered from dandelionPlot.Rmd in trackViewer 1.41.3.
| Epistatic Nested Effects Models: | Inferring mixed epistasis from indirect measurements of knock-out screensUpdated 3 years ago

Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz

Rendered from epiNEM.Rmd in epiNEM 1.29.0.
Normalizing single-cell RNA-seq dataUpdated 3 years ago

Aaron Lun

Rendered from norm.Rmd in scuttle 1.15.1.
Quality control for single-cell RNA-seq dataUpdated 3 years ago

Aaron Lun

Rendered from qc.Rmd in scuttle 1.15.1.
Matrix representations to support decompositionUpdated 3 years ago

Aaron Lun

Rendered from representations.Rmd in BiocSingular 1.21.2.
| Mixture Nested Effects Models: | Simultaneous inference of causal networks and corresponding subpopulations from single cell perturbation dataUpdated 4 years ago

Martin Pirkl, Niko Beerenwinkel

Rendered from mnem.Rmd in mnem 1.21.0.
glmGamPoi QuickstartUpdated 4 years ago

Constantin Ahlmann-Eltze

Rendered from glmGamPoi.Rmd in glmGamPoi 1.17.3.
新手指引Updated 4 years ago

Jiefei Wang

Rendered from quick_start_guide_Chinese.Rmd in SharedObject 1.19.1.
A quick introduction to GRanges and GRangesList objects (slides)Updated 4 years ago

Hervé Pagès

Rendered from GRanges_and_GRangesList_slides.Rnw in GenomicRanges 1.57.1.
A quick overview of the S4 class systemUpdated 4 years ago

Hervé Pagès

Rendered from S4QuickOverview.Rnw in S4Vectors 0.43.1.
DOSE: Disease Ontology Semantic and Enrichment analysisUpdated 4 years ago

Guangchuang Yu

Rendered from DOSE.Rmd in DOSE 3.31.2.
Functional analysis of mouse mammary gland RNA-SeqUpdated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

Rendered from mouse_bioconductor.Rmd in ViSEAGO 1.19.0.
An overview of ViSEAGO: Visualisation, Semantic similarity, Enrichment Analysis of Gene Ontology.Updated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

Rendered from ViSEAGO.Rmd in ViSEAGO 1.19.0.
Functional analysis of mouse mammary gland RNA-Seq using fgsea instead of topGOUpdated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

Rendered from fgsea_alternative.Rmd in ViSEAGO 1.19.0.
Evaluate impact of Semantic Similiarity choiceUpdated 4 years ago

Aurelien Brionne, Amelie Juanchich, Christelle Hennequet-Antier

Rendered from SS_choice.Rmd in ViSEAGO 1.19.0.
GenomeInfoDb: Introduction to GenomeInfoDbUpdated 4 years ago

Hervé Pagès

Rendered from GenomeInfoDb.Rnw in GenomeInfoDb 1.41.1.
Example of a cytometry data analysis with DepecheRUpdated 4 years ago

Jakob Theorell

Rendered from DepecheR_test.Rmd in DepecheR 1.21.3.
sparseMatrixStatsUpdated 4 years ago

Constantin Ahlmann-Eltze

Rendered from sparseMatrixStats.Rmd in sparseMatrixStats 1.17.2.
Dockstore and Bioconductor for AnVILUpdated 4 years ago

BJ Stubbs, S Gopaulakrishnan, Nitesh Truaga, Martin Morgan, Vincent Carey

Rendered from BiocDockstore.Rmd in AnVIL 1.17.6.
The Shiny Variant ExplorerUpdated 4 years ago

Kévin Rue-Albrecht

Rendered from tSVE.Rmd in TVTB 1.31.1.
Automatic Statistical Identification in Complex Spectra (ASICS)Updated 4 years ago

Gaëlle Lefort, Rémi Servien and Nathalie Vialaneix

Rendered from ASICS.Rmd in ASICS 2.21.1.
Using pRoloc for spatial proteomics data analysisUpdated 4 years ago

Lisa M. Breckels, Laurent Gatto

Rendered from v01-pRoloc-tutorial.Rmd in pRoloc 1.45.1.
oligo User's GuideUpdated 4 years ago

Benilton Carvalho

Rendered from oug.Rnw in oligo 1.69.2.
Probability plot usageUpdated 5 years ago

Jakob Theorell

Rendered from GroupProbPlot_usage.Rmd in DepecheR 1.21.3.
Annotating spatial proteomics dataUpdated 5 years ago

Lisa M. Breckels, Laurent Gatto

Rendered from v04-pRoloc-goannotations.Rmd in pRoloc 1.45.1.
Bayesian Analysis of Spatial Proteomics data using pRolocUpdated 5 years ago

Oliver Crook, Laurent Gatto

Rendered from v03-pRoloc-bayesian.Rmd in pRoloc 1.45.1.
Singular value decomposition for Bioconductor packagesUpdated 5 years ago

Aaron Lun

Rendered from decomposition.Rmd in BiocSingular 1.21.2.
Machine learning techniques available in pRolocUpdated 5 years ago

Laurent Gatto

Rendered from v02-pRoloc-ml.Rmd in pRoloc 1.45.1.
QC-free approach with Combat methodUpdated 5 years ago

Hemi Luan

Rendered from Combat.Rmd in statTarget 1.35.1.
pathway analysis (mummichog)Updated 5 years ago

Hemi Luan

Rendered from pathway_analysis.Rmd in statTarget 1.35.1.
Extending the SummarizedExperiment classUpdated 6 years ago

Aaron Lun

Rendered from Extensions.Rmd in SummarizedExperiment 1.35.1.
The bigmelon PackageUpdated 6 years ago

Leonard C. Schalkwyk

Rendered from bigmelon.Rnw in bigmelon 1.31.1.
Introduction to TVTBUpdated 6 years ago

Kévin Rue-Albrecht

Rendered from Introduction.Rmd in TVTB 1.31.1.
An Overview of the IRanges packageUpdated 6 years ago

Hervé Pagès

Rendered from IRangesOverview.Rnw in IRanges 2.39.1.
Bioconductor LaTeX Style 2.0Updated 6 years ago

Bioconductor Package

Rendered from LatexStyle2.Rnw in BiocStyle 2.33.1.
Cheatsheet for MultiAssayExperimentUpdated 7 years ago

Marcel Ramos

Rendered from MultiAssayExperiment_cheatsheet.pdf.asis in MultiAssayExperiment 1.31.3.
Extending GenomicRangesUpdated 8 years ago

Hervé Pagès

Rendered from ExtendingGenomicRanges.Rnw in GenomicRanges 1.57.1.
Basic DESeq2 results explorationUpdated NaN years ago

Leonardo Collado-Torres

Rendered from SRP009615-results.Rmd in recount 1.31.2.
The PIUMA package - Phenotypes Identification Using Mapper from topological data AnalysisUpdated 2 months ago

Mattia Chiesa, Laura Ballarini, Alessia Gerbasi, Giuseppe Albi, Arianna Dagliati, Luca Piacentini

Rendered from PIUMA_vignette.Rmd in PIUMA 1.1.1.
Introduction to the SpatialFeatureExperiment classUpdated 2 months ago

Lambda Moses, Lior Pachter

Rendered from SFE.Rmd in SpatialFeatureExperiment 1.7.0.
Questions and answers from over the yearsUpdated 2 months ago

Sean Davis

Rendered from questions-and-answers.Rmd in GenomicDataCommons 1.29.3.
funOmicsUpdated 2 months ago

Elisa Gómez de Lope

Rendered from funomics_vignette.Rmd in funOmics 0.99.8.
The GenomicDataCommons PackageUpdated 2 months ago

Sean Davis & Martin Morgan

Rendered from overview.Rmd in GenomicDataCommons 1.29.3.
Working with simple somatic mutationsUpdated 2 months ago

Sean Davis

Rendered from somatic_mutations.Rmd in GenomicDataCommons 1.29.3.
Annotation of MS-based Metabolomics DataUpdated 2 months ago

Johannes Rainer

Rendered from MetaboAnnotation.Rmd in MetaboAnnotation 1.9.1.
HicAggR - In depth tutorialUpdated 2 months ago

Nicolas Chanard, David Depierre, Robel A. Tesfaye, Stéphane Schaak & Olivier Cuvier

Rendered from HicAggR.Rmd in HicAggR 1.1.2.
BREW3R.rUpdated 3 months ago

Lucille Lopez-Delisle

Rendered from BREW3R.r.Rmd in BREW3R.r 1.1.1.
Low Dimensional Projection of Cytometry SamplesUpdated 4 months ago

Philippe Hauchamps, Laurent Gatto

Rendered from CytoMDS.Rmd in CytoMDS 1.1.0.
User's GuideUpdated 4 months ago

Shian Su

Rendered from UsersGuide.Rmd in NanoMethViz 3.1.5.
A brief introduction to edgeRUpdated 5 months ago

Yunshun Chen

Rendered from intro.Rmd in edgeR 4.3.4.
Overview of the tidybulk packageUpdated 8 months ago

Stefano Mangiola

Rendered from introduction.Rmd in tidybulk 1.17.0.
Introduction to shiny.goslingUpdated 9 months ago

Appsilon

Rendered from intro.Rmd in shiny.gosling 1.1.0.
Using a GRanges object in shiny.goslingUpdated 9 months ago

Appsilon

Rendered from GRanges.Rmd in shiny.gosling 1.1.0.
Creating a Circos Plot with VCF DataUpdated 9 months ago

Appsilon

Rendered from VCF.Rmd in shiny.gosling 1.1.0.
Creating an Interactive Line Chart with shiny.goslingUpdated 9 months ago

Appsilon

Rendered from lineChart.Rmd in shiny.gosling 1.1.0.
Creating a Multi-Scale Sequence TrackUpdated 9 months ago

Appsilon

Rendered from textAnnotation.Rmd in shiny.gosling 1.1.0.
Overview of the tidySingleCellExperiment packageUpdated 10 months ago

Stefano Mangiola

Rendered from introduction.Rmd in tidySingleCellExperiment 1.15.1.
scDesign3 QuickstartUpdated 10 months ago

Dongyuan Song, Qingyang Wang

Rendered from scDesign3.Rmd in scDesign3 1.3.0.
LC-MS/MS data processing and spectral matching workflow using msPurity and XCMSUpdated 10 months ago

Thomas N. Lawson

Rendered from msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd in msPurity 1.31.1.
edgeR User's GuideUpdated 1 years ago

Yunshun Chen

Rendered from edgeRUsersGuide.Rnw in edgeR 4.3.4.
ChIPseeker: an R package for ChIP peak Annotation, Comparison and VisualizationUpdated 1 years ago

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered from ChIPseeker.Rmd in ChIPseeker 1.41.0.
OpenCyto: How to use different auto gating functionsUpdated 2 years ago

Mike Jiang

Rendered from HowToAutoGating.Rmd in openCyto 2.17.1.
An Introduction to the openCyto packageUpdated 2 years ago

Mike Jiang

Rendered from openCytoVignette.Rmd in openCyto 2.17.1.
New Implementation of the HIBAG Algorithm with Latest Intel IntrinsicsUpdated 2 years ago

Dr. Xiuwen Zheng

Rendered from Implementation.Rmd in HIBAG 1.41.1.
HIBAG -- an R Package for HLA Genotype Imputation with Attribute BaggingUpdated 2 years ago

Dr. Xiuwen Zheng

Rendered from HIBAG.Rmd in HIBAG 1.41.1.
HIBAG -- an R Package for HLA Genotype Imputation with Attribute BaggingUpdated 2 years ago

Dr. Xiuwen Zheng

Rendered from HLA_Association.Rmd in HIBAG 1.41.1.
Regression Based Approach for Motif SelectionUpdated 2 years ago

Dania Machlab, Lukas Burger, Charlotte Soneson, Michael Stadler

Rendered from selecting_motifs_with_randLassoStabSel.Rmd in monaLisa 1.11.1.
Using msPurity for Precursor Ion Purity Assessments, Data Processing and Metabolite Annotation of Mass Spectrometry Fragmentation DataUpdated 3 years ago

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