DESeq2

DOI:10.18129/B9.bioc.DESeq2

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seeDESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 3.14

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

Installation

To install this package, start R (version "4.1") 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")

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

Details

biocViews	Bayesian,ChIPSeq,Clustering,DifferentialExpression,GeneExpression,ImmunoOncology,Normalization,PrincipalComponent,RNASeq,Regression,Sequencing,Software,Transcription
Version	1.34.0
In Bioconductor since	BioC 2.12 (R-3.0) (9 years)
License	LGPL (>= 3)
Depends	S4Vectors(>= 0.23.18),IRanges,GenomicRanges,SummarizedExperiment(>= 1.1.6)
Imports	BiocGenerics(>= 0.7.5),Biobase,BiocParallel,genefilter, methods, stats4,locfit,geneplotter,ggplot2,Rcpp(>= 0.11.0)
LinkingTo	Rcpp,RcppArmadillo
Suggests	testthat,knitr,rmarkdown,vsn,pheatmap,RColorBrewer,apeglm,ashr,tximport,tximeta,tximportData,readr,pbapply,airway,pasilla(>= 0.2.10),glmGamPoi,BiocManager
SystemRequirements
Enhances
URL	https://github.com/mikelove/DESeq2
Depends On Me	DEWSeq,DEXSeq,metaseqR2,rgsepd,rnaseqDTU,rnaseqGene,SeqGSEA,TCC,tRanslatome
Imports Me	Anaquin,animalcules,anota2seq,APAlyzer,benchdamic,BioNERO,BloodCancerMultiOmics2017,BRGenomics,CeTF,circRNAprofiler,consensusDE,coseq,countsimQC,crossmeta,DaMiRseq,debrowser,DEComplexDisease,DEFormats,DEGreport,deltaCaptureC,DEsubs,DiffBind,easier,EBSEA,eegc,ERSSA,exomePeak2,ExpHunterSuite,FieldEffectCrc,GDCRNATools,GeneTonic,GenoGAM,Glimma,HTSFilter,icetea,ideal,IHWpaper,INSPEcT,IntEREst,isomiRs,kissDE,microbiomeExplorer,microbiomeMarker,MLSeq,multiSight,muscat,NBAMSeq,ORFik,OUTRIDER,PathoStat,pcaExplorer,phantasus,proActiv,recountWorkflow,RegEnrich,regionReport,ReportingTools,RiboDiPA,Rmmquant,RNASeqR,scBFA,scGPS,SEtools,singleCellTK,SNPhood,spatialHeatmap,srnadiff,systemPipeTools,TBSignatureProfiler,TimeSeriesExperiment,UMI4Cats,vidger,vulcan
Suggests Me	aggregateBioVar,apeglm,bambu,biobroom,BiocGenerics,BioCor,BiocSet,CAGEr,CAGEWorkflow,compcodeR,curatedAdipoChIP,curatedAdipoRNA,dearseq,derfinder,diffloop,dittoSeq,EDASeq,EnhancedVolcano,EnrichmentBrowser,fishpond,fluentGenomics,gage,GenomicAlignments,GenomicRanges,glmGamPoi,HiCDCPlus,IHW,InteractiveComplexHeatmap,miRmine,NxtIRFcore,OPWeight,PCAtools,phyloseq,progeny,PROPER,recount,RegParallel,RUVSeq,scran,Single.mTEC.Transcriptomes,sparrow,subSeq,SummarizedBenchmark,systemPipeR,systemPipeShiny,TFEA.ChIP,tidybulk,topconfects,tximeta,tximport,variancePartition,Wrench,zinbwave
Links To Me
Build Report

Package Archives

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Source Package	DESeq2_1.34.0.tar.gz
Windows Binary	DESeq2_1.34.0.zip(32- & 64-bit)
macOS 10.13 (High Sierra)	DESeq2_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DESeq2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DESeq2
Package Short Url	//www.anjoumacpherson.com/packages/DESeq2/
Package Downloads Report	Download Stats