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Bioconductor - DESeq2

DESeq2

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

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.21)

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")

Details biocViews Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription Version 1.48.1 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 See More 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, CeTF, circRNAprofiler, CleanUpRNAseq, consensusDE, coseq, countsimQC, cypress, DaMiRseq, debrowser, DEFormats, DEGreport, DELocal, deltaCaptureC, DEsubs, DiffBind, easier, EBSEA, ERSSA, GDCRNATools, GeneTonic, gg4way, Glimma, GRaNIE, hermes, HTSFilter, HybridExpress, icetea, ideal, INSPEcT, IntEREst, iSEEde, isomiRs, 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, scQTLtools, 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, PCAtools, phyloseq, progeny, QRscore, raer, recount, ribosomeProfilingQC, roastgsa, RUVSeq, Rvisdiff, scran, sparrow, spatialHeatmap, SpliceWiz, subSeq, systemPipeR, systemPipeShiny, TFEA.ChIP, tidybulk, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave, curatedAdipoChIP, curatedAdipoRNA, GSE62944, RegParallel, Single.mTEC.Transcriptomes, CAGEWorkflow, fluentGenomics, bakR, cellpypes, conos, FateID, ggpicrust2, GiANT, glmmSeq, grandR, lfc, LorMe, metacoder, metaRNASeq, MiscMetabar, 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.

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