DESeq2

This is the development version of DESeq2; for the stable release version, see DESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Development (3.24)

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], Anqi Zhu [ctb], Nikolaos Ignatiadis [ctb], Raphael Rossellini [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, enter citation("DESeq2")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("DESeq2")

For older versions of R, please refer to the appropriate Bioconductor 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	1.53.2
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 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, APAlyzer, BatchQC, benchdamic, broadSeq, carnation, CeTF, circRNAprofiler, CleanUpRNAseq, coseq, countsimQC, cypress, DaMiRseq, debrowser, DeeDeeExperiment, DEFormats, DEGreport, DELocal, deltaCaptureC, DEsubs, DiffBind, DOtools, DOTSeq, DspikeIn, easier, EBSEA, ERSSA, fourSynergy, GDCRNATools, GeneTonic, gg4way, Glimma, GRaNIE, hermes, HTSFilter, HybridExpress, icetea, ideal, INSPEcT, IntEREst, iSEEde, isomiRs, kissDE, magpie, microbiomeExplorer, MIRit, MLSeq, mobileRNA, mosdef, MultiRNAflow, NBAMSeq, NetActivity, ORFik, OUTRIDER, pairedGSEA, PathoStat, pcaExplorer, phantasus, POMA, proActiv, RegEnrich, regionReport, ReportingTools, RiboDiPA, Rmmquant, saseR, scBFA, scECODA, scGPS, scQTLtools, SEtools, singleCellTK, SNPhood, srnadiff, SurfR, systemPipeTools, TBSignatureProfiler, TEKRABber, terapadog, UMI4Cats, vidger, VISTA, vulcan, zitools, BloodCancerMultiOmics2017, FieldEffectCrc, IHWpaper, ExpHunterSuite, recountWorkflow, autoGO, cinaR, ExpGenetic, HEssRNA, limorhyde2, microbial, power.nb, RCPA, RNAseqQC, sRNAGenetic, TransProR, wilson, XYomics
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, muscat, OPWeight, pathlinkR, PCAtools, phyloseq, progeny, QRscore, raer, recount, RFGeneRank, ribosomeProfilingQC, roastgsa, RUVSeq, Rvisdiff, scran, scToppR, sparrow, spatialHeatmap, 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, futurize, genefindr, ggpicrust2, GiANT, glmmSeq, grandR, IOBR, lfc, LorMe, metacoder, metaRNASeq, MiscMetabar, myTAI, pctax, pmartR, RaceID, rliger, seqgendiff, Seurat, SeuratExplorer, venny, volcano3D
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DESeq2_1.53.2.tar.gz
Windows Binary (x86_64)	DESeq2_1.53.2.zip
macOS Binary (big-sur-x86_64)	DESeq2_1.53.2.tgz
macOS Binary (sonoma-arm64)	DESeq2_1.53.2.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