Bioconductor – DESeq2

DOI: 10.18129/B9.bioc.DESeq2  


This package is for version 3.10 of Bioconductor;
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Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 3.10

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], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Maintainer: Michael Love <michaelisaiahlove at>

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biocViews Bayesian, ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, PrincipalComponent, RNASeq, Regression, Sequencing, Software, Transcription
Version 1.26.0
In Bioconductor since BioC 2.12 (R-3.0) (7 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, Hmisc, Rcpp (>= 0.11.0)
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla(>= 0.2.10)
Depends On Me DChIPRep, DEWSeq, DEXSeq, FourCSeq, rgsepd, rnaseqDTU, rnaseqGene, TCC, XBSeq
Imports Me anamiR, Anaquin, animalcules, anota2seq, BloodCancerMultiOmics2017, circRNAprofiler, consensusDE, coseq, countsimQC, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, deltaCaptureC, DEsubs, DiffBind, eegc, ERSSA, FourCSeq, GDCRNATools, GenoGAM, HTSFilter, icetea, ideal, IHWpaper, ImpulseDE2, INSPEcT, IntEREst, isomiRs, JunctionSeq, kissDE, MLSeq, muscat, NBAMSeq, ORFik, OUTRIDER, PathoStat, pcaExplorer, PowerExplorer, recountWorkflow, regionReport, ReportingTools, Rmmquant, RNASeqR, scBFA, singleCellTK, SNPhood, srnadiff, systemPipeR, TimeSeriesExperiment, vidger
Suggests Me apeglm, biobroom, BiocGenerics, BioCor, BiocSet, CAGEr, CAGEWorkflow, compcodeR, curatedAdipoChIP, curatedAdipoRNA, derfinder, diffloop, EnhancedVolcano, fishpond, gage, GenomicAlignments, GenomicRanges, Glimma, IHW, JctSeqData, miRmine, OPWeight, phyloseq, progeny, recount, RegParallel, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, SummarizedBenchmark, TFEA.ChIP, ToPASeq, topconfects, tximeta, tximport, variancePartition, Wrench, zinbwave
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