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Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: Release (3.18)

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.

Author: Yunshun Chen, Aaron TL Lun, Davis J McCarthy, Lizhong Chen, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth

Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>, Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>, Mark Robinson <mark.robinson at imls.uzh.ch>

Citation (from within R, enter citation("edgeR")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

A brief introduction to edgeR HTML R Script
edgeR User's Guide PDF
Reference Manual PDF


biocViews AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, Coverage, DNAMethylation, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, QualityControl, RNASeq, Regression, SAGE, Sequencing, SingleCell, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version 4.0.16
In Bioconductor since BioC 2.3 (R-2.8) (15.5 years)
License GPL (>=2)
Depends R (>= 3.6.0), limma(>= 3.41.5)
Imports methods, graphics, stats, utils, locfit, Rcpp
System Requirements
URL https://bioinf.wehi.edu.au/edgeR/ https://bioconductor.org/packages/edgeR
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Suggests jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject
Linking To Rcpp
Depends On Me ASpli, EGSEA123, IntEREst, methylMnM, miloR, octad, ReactomeGSA.data, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, RnaSeqSampleSizeData, RUVSeq, TCC, tRanslatome
Imports Me affycoretools, anota2seq, ATACseqQC, autonomics, AWFisher, baySeq, beer, benchdamic, BioQC, censcyt, ChromSCape, circRNAprofiler, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, crossmeta, csaw, DaMiRseq, dce, debrowser, DEFormats, DEGreport, DESpace, DEsubs, diffcyt, diffHic, diffUTR, DMRcate, doseR, dreamlet, DRIMSeq, DropletUtils, easyRNASeq, eegc, EGSEA, eisaR, emtdata, EnrichmentBrowser, erccdashboard, ERSSA, ExpHunterSuite, extraChIPs, GDCRNATools, GenomicPlot, GEOexplorer, gg4way, Glimma, GSEABenchmarkeR, hermes, HTSFilter, icetea, infercnv, iSEEde, IsoformSwitchAnalyzeR, KnowSeq, Maaslin2, mastR, MEB, MEDIPS, metaseqR2, microbiomeMarker, MLSeq, moanin, Motif2Site, msgbsR, msmsTests, multiHiCcompare, muscat, PathoStat, phantasus, PhIPData, ppcseq, PROPER, psichomics, RCM, recountWorkflow, regsplice, Repitools, ReportingTools, RNAseqCovarImpute, RnaSeqSampleSize, ROSeq, Rvisdiff, scCB2, scde, scone, scran, ScreenR, SEtools, SIMD, SingleCellSignalR, singscore, SingscoreAMLMutations, sparrow, spatialHeatmap, spatialLIBD, speckle, splatter, SPsimSeq, srnadiff, sSNAPPY, standR, STATegRa, sva, TBSignatureProfiler, TCseq, tradeSeq, treekoR, tweeDEseq, vidger, xcore, yarn, zinbwave
Suggests Me ABSSeq, bigPint, biobroom, CAGEWorkflow, chipseqDB, ClassifyR, cqn, cydar, dcanr, dearseq, DEScan2, DiffBind, dittoSeq, DSS, easyreporting, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, GeoTcgaData, glmGamPoi, goseq, groHMM, GSAR, GSVA, ideal, iSEEpathways, iSEEu, leeBamViews, lemur, missMethyl, MoonlightR, multiMiR, raer, recount, regionReport, ribosomeProfilingQC, satuRn, scider, SeqGate, signifinder, SpliceWiz, stageR, subSeq, SummarizedBenchmark, systemPipeR, TCGAbiolinks, tidybulk, topconfects, tximeta, tximport, variancePartition, weitrix, Wrench, zenith, zFPKM
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Source Package edgeR_4.0.16.tar.gz
Windows Binary edgeR_4.0.16.zip (64-bit only)
macOS Binary (x86_64) edgeR_4.0.16.tgz
macOS Binary (arm64) edgeR_4.0.16.tgz
Source Repository git clone https://git.bioconductor.org/packages/edgeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/edgeR
Bioc Package Browser https://code.bioconductor.org/browse/edgeR/
Package Short Url https://bioconductor.org/packages/edgeR/
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Old Source Packages for BioC 3.18 Source Archive