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

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: Development (3.20)

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, Pedro Baldoni, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth

Maintainer: Yunshun Chen <yuchen at>, Gordon Smyth <smyth at>, Aaron Lun <infinite.monkeys.with.keyboards at>, Mark Robinson <mark.robinson at>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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 4.3.5
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
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Suggests jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment,, Matrix, SeuratObject
Linking To Rcpp
Depends On Me ASpli, IntEREst, methylMnM, miloR, octad, RUVSeq, TCC, tRanslatome,, EGSEA123, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, csawBook, OSCA.advanced, OSCA.multisample, OSCA.workflows, babel, BALLI, BioInsight, SCdeconR
Imports Me affycoretools, ATACseqQC, autonomics, AWFisher, baySeq, beer, benchdamic, BioQC, broadSeq, censcyt, ChromSCape, circRNAprofiler, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, crossmeta, csaw, cypress, DaMiRseq, Damsel, dce, debrowser, DEFormats, DEGreport, DESpace, DEsubs, diffcyt, diffHic, diffUTR, dinoR, DMRcate, doseR, dreamlet, DRIMSeq, DropletUtils, EGSEA, eisaR, EnrichmentBrowser, erccdashboard, ERSSA, extraChIPs, GDCRNATools, GenomicPlot, GEOexplorer, gg4way, Glimma, GSEABenchmarkeR, hermes, HTSFilter, icetea, infercnv, iSEEde, IsoformSwitchAnalyzeR, KnowSeq, Maaslin2, mastR, MEB, MEDIPS, metaseqR2, microbiomeMarker, MIRit, MLSeq, moanin, mobileRNA, MOSim, Motif2Site, msmsTests, multiHiCcompare, muscat, PathoStat, phantasus, PhIPData, ppcseq, PROPER, psichomics, RCM, regsplice, Repitools, RNAseqCovarImpute, ROSeq, Rvisdiff, saseR, scCB2, scde, scone, scran, ScreenR, SEtools, SIMD, SingleCellSignalR, singscore, spatialHeatmap, speckle, splatter, SPsimSeq, srnadiff, sSNAPPY, standR, STATegRa, SurfR, sva, TBSignatureProfiler, TCseq, tradeSeq, treeclimbR, treekoR, tweeDEseq, vidger, xcore, yarn, zinbwave, emtdata, spatialLIBD, ExpHunterSuite, recountWorkflow, SingscoreAMLMutations, aIc, bulkAnalyseR, CAMML, cinaR, CoreMicrobiomeR, ggpicrust2, HTSCluster, MetaLonDA, microbial, myTAI, RCPA, RVA, scITD, SCRIP, scRNAtools, SPUTNIK, ssizeRNA, TSGS
Suggests Me ABSSeq, biobroom, ClassifyR, cqn, cydar, dcanr, dearseq, DEScan2, DiffBind, dittoSeq, DSS, easyreporting, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, GeoTcgaData, glmGamPoi, goseq, groHMM, GSAR, GSVA, ideal, iSEEpathways, iSEEu, lemur, missMethyl, MoonlightR, multiMiR, raer, recount, regionReport, ribosomeProfilingQC, satuRn, scider, SeqGate, SpliceWiz, stageR, subSeq, systemPipeR, TCGAbiolinks, tidybulk, topconfects, tximeta, tximport, variancePartition, weitrix, Wrench, zenith, zFPKM, leeBamViews, CAGEWorkflow, chipseqDB, DGEobj, DGEobj.utils, DiPALM, glmmSeq, MiscMetabar, pctax, pmartR, seqgendiff, SIBERG, volcano3D
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