DESeq2

This is thereleased version of DESeq2; for the devel version, seeDESeq2.

Differential gene expression analysis based on the negative binomial distribution

DOI: 10.18129/B9.bioc.DESeq2

Bioconductor version: Release (3.22)

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.

Author: Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Citation (from within R, entercitation("DESeq2")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("DESeq2")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DESeq2")

Analyzing RNA-seq data with DESeq2	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian,ChIPSeq,Clustering,DifferentialExpression,GeneExpression,ImmunoOncology,Normalization,PrincipalComponent,RNASeq,Regression,Sequencing,Software,Transcription
Version	1.50.2
In Bioconductor since	BioC 2.12 (R-3.0) (12.5 years)
License	LGPL (>= 3)
Depends	S4Vectors(>= 0.23.18),IRanges,GenomicRanges,SummarizedExperiment(>= 1.1.6)
Imports	BiocGenerics(>= 0.7.5),Biobase,BiocParallel,matrixStats, methods, stats4,locfit,ggplot2 (>= 3.4.0),Rcpp (>= 0.11.0),MatrixGenerics
System Requirements
URL	https://github.com/thelovelab/DESeq2

Suggests	testthat,knitr,rmarkdown,vsn,pheatmap,RColorBrewer,apeglm,ashr,tximport,tximeta,tximportData,readr,pbapply,airway,glmGamPoi,BiocManager
Linking To	Rcpp,RcppArmadillo
Enhances
Depends On Me	DEWSeq,DEXSeq,metaseqR2,octad,rgsepd,SeqGSEA,TCC,tRanslatome,rnaseqDTU,rnaseqGene,Anaconda,DRomics,ordinalbayes
Imports Me	Anaquin,animalcules,BatchQC,CeTF,circRNAprofiler,CleanUpRNAseq,consensusDE,coseq,countsimQC,cypress,DaMiRseq,debrowser,DeeDeeExperiment,DEFormats,DEGreport,deltaCaptureC,DEsubs,DiffBind,DOtools,DspikeIn,easier,EBSEA,ERSSA,GDCRNATools,GeneTonic,gg4way,Glimma,GRaNIE,hermes,HTSFilter,HybridExpress,icetea,ideal,INSPEcT,IntEREst,iSEEde,kissDE,magpie,microbiomeExplorer,MIRit,MLSeq,mobileRNA,mosdef,MultiRNAflow,muscat,NBAMSeq,NetActivity,ORFik,OUTRIDER,pairedGSEA,PathoStat,pcaExplorer,phantasus,POMA,proActiv,RegEnrich,regionReport,ReportingTools,RiboDiPA,Rmmquant,saseR,scBFA,scGPS,SEtools,singleCellTK,SNPhood,srnadiff,SurfR,systemPipeTools,TBSignatureProfiler,TEKRABber,terapadog,UMI4Cats,vidger,vulcan,zitools,BloodCancerMultiOmics2017,FieldEffectCrc,homosapienDEE2CellScore,IHWpaper,ExpHunterSuite,recountWorkflow,autoGO,bulkAnalyseR,cinaR,ExpGenetic,HEssRNA,limorhyde2,microbial,RCPA,RNAseqQC,sRNAGenetic,TransProR,wilson
Suggests Me	aggregateBioVar,apeglm,bambu,BindingSiteFinder,biobroom,BiocGenerics,BioCor,BiocSet,BioNERO,CAGEr,compcodeR,dar,dearseq,derfinder,dittoSeq,EDASeq,EnhancedVolcano,EnrichmentBrowser,EWCE,extraChIPs,fishpond,gage,GeDi,GenomicAlignments,GenomicRanges,GeoTcgaData,geyser,glmGamPoi,HiCDCPlus,IHW,InteractiveComplexHeatmap,methodical,OPWeight,pathlinkR,phyloseq,progeny,QRscore,raer,recount,ribosomeProfilingQC,roastgsa,RUVSeq,Rvisdiff,scran,sparrow,SpliceWiz,subSeq,systemPipeR,systemPipeShiny,TFEA.ChIP,tidybulk,topconfects,tximeta,tximport,variancePartition,Wrench,zinbwave,ChIPDBData,curatedAdipoChIP,curatedAdipoRNA,GSE62944,RegParallel,Single.mTEC.Transcriptomes,CAGEWorkflow,fluentGenomics,seqpac,bakR,conos,dependentsimr,FateID,ggpicrust2,GiANT,glmmSeq,grandR,lfc,LorMe,metaRNASeq,MiscMetabar,myTAI,pctax,pmartR,RaceID,rliger,SCdeconR,seqgendiff,Seurat,SeuratExplorer,volcano3D
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	DESeq2_1.50.2.tar.gz
Windows Binary (x86_64)	DESeq2_1.50.2.zip (64-bit only)
macOS Binary (x86_64)	DESeq2_1.50.2.tgz
macOS Binary (arm64)	DESeq2_1.50.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DESeq2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DESeq2
Bioc Package Browser	https://code.bioconductor.org/browse/DESeq2/
Package Short Url	https://bioconductor.org/packages/DESeq2/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.22	Source Archive

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