DOI: 10.18129/B9.bioc.edgeR    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see edgeR.

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: 3.10

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 counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.

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

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

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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:



PDF edgeR Vignette
PDF edgeRUsersGuide.pdf
PDF   Reference Manual
Text   NEWS


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, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version 3.28.1
In Bioconductor since BioC 2.3 (R-2.8) (11.5 years)
License GPL (>=2)
Depends R (>= 3.6.0), limma(>= 3.41.5)
Imports graphics, stats, utils, methods, locfit, Rcpp
LinkingTo Rcpp
Suggests AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines
SystemRequirements C++11
URL http://bioinf.wehi.edu.au/edgeR
Depends On Me ASpli, DBChIP, EDDA, EGSEA123, IntEREst, manta, methylMnM, ReactomeGSA.data, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, RNASeqR, RnaSeqSampleSizeData, RUVSeq, samExploreR, TCC, tRanslatome
Imports Me affycoretools, anota2seq, ArrayExpressHTS, ATACseqQC, AWFisher, baySeq, BioQC, circRNAprofiler, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, csaw, DaMiRseq, debrowser, DEComplexDisease, DEFormats, DEGreport, DEsubs, DiffBind, diffcyt, diffHic, diffloop, DMRcate, doseR, DRIMSeq, DropletUtils, easyRNASeq, EBSEA, EDDA, eegc, EGSEA, EnrichmentBrowser, erccdashboard, ERSSA, GDCRNATools, Glimma, GSEABenchmarkeR, HTSFilter, icetea, infercnv, IsoformSwitchAnalyzeR, KnowSeq, Maaslin2, MEDIPS, metaseqR, MIGSA, MLSeq, msgbsR, msmsTests, multiHiCcompare, muscat, NBSplice, PathoStat, PROPER, psichomics, RCM, recountWorkflow, regsplice, Repitools, ReportingTools, rnaSeqMap, RnaSeqSampleSize, scde, scone, scran, SIMD, singscore, SingscoreAMLMutations, splatter, STATegRa, SVAPLSseq, systemPipeR, TCGAbiolinks, TCseq, TimeSeriesExperiment, tradeSeq, tweeDEseq, vidger, yarn, zinbwave
Suggests Me ABSSeq, bigPint, biobroom, BitSeq, CAGEWorkflow, chipseqDB, ClassifyR, clonotypeR, cqn, csawUsersGuide, cydar, dcanr, DEScan2, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, goseq, groHMM, GSAR, GSVA, ideal, JctSeqData, leeBamViews, missMethyl, multiMiR, regionReport, SSPA, stageR, subSeq, SummarizedBenchmark, ToPASeq, topconfects, tximeta, tximport, variancePartition, Wrench, zFPKM
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package edgeR_3.28.1.tar.gz
Windows Binary edgeR_3.28.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) edgeR_3.28.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/edgeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/edgeR
Package Short Url https://bioconductor.org/packages/edgeR/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: