DESeq2

This is the released version of DESeq2; for the devel version, see DESeq2.

Differential gene expression analysis based on the negative binomial distribution

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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, enter citation("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 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 1.50.2

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, 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

Follow Installation 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

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/

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Old Source Packages for BioC 3.22 Source Archive