edgeR

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 (3.21)

Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.

Author: Yunshun Chen, Lizhong Chen, Aaron TL Lun, Davis J McCarthy, Pedro Baldoni, 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")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("edgeR")

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("edgeR")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, Coverage, DNAMethylation, DifferentialExpression, DifferentialMethylation, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, Proteomics, QualityControl, RNASeq, Regression, SAGE, Sequencing, SingleCell, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version	4.5.6
In Bioconductor since	BioC 2.3 (R-2.8) (16.5 years)
License	GPL (>=2)
Depends	R (>= 3.6.0), limma(>= 3.63.6)
Imports	methods, graphics, stats, utils, locfit
System Requirements
URL	https://bioinf.wehi.edu.au/edgeR/ https://bioconductor.org/packages/edgeR

Suggests	jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db, SummarizedExperiment
Linking To
Enhances
Depends On Me	ASpli, methylMnM, miloR, octad, RUVSeq, TCC, tRanslatome, ReactomeGSA.data, EGSEA123, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, csawBook, OSCA.multisample, OSCA.workflows, babel, BALLI, BioInsight, SCdeconR
Imports Me	affycoretools, ATACseqQC, autonomics, AWFisher, baySeq, beer, benchdamic, BioQC, broadSeq, censcyt, ChromSCape, circRNAprofiler, CleanUpRNAseq, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, csaw, cypress, DaMiRseq, Damsel, dce, debrowser, DEFormats, DEGreport, DESpace, DEsubs, diffcyt, diffHic, dinoR, DMRcate, doseR, dreamlet, DRIMSeq, DropletUtils, easyRNASeq, EGSEA, eisaR, EnrichmentBrowser, erccdashboard, ERSSA, extraChIPs, GDCRNATools, GenomicPlot, GEOexplorer, gg4way, gINTomics, Glimma, GSEABenchmarkeR, hermes, HTSFilter, icetea, infercnv, iSEEde, KnowSeq, Maaslin2, mastR, MEB, MEDIPS, metaseqR2, MIRit, MLSeq, moanin, mobileRNA, MOSim, Motif2Site, msgbsR, msmsTests, multiHiCcompare, muscat, PathoStat, phantasus, PhIPData, ppcseq, PRONE, PROPER, psichomics, RCM, regsplice, Repitools, RNAseqCovarImpute, ROSeq, Rvisdiff, scCB2, scde, scone, scran, ScreenR, SEtools, SIMD, SingleCellSignalR, singscore, SpaNorm, sparrow, 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, CIDER, cinaR, CoreMicrobiomeR, HTSCluster, idiffomix, microbial, RCPA, RVA, scITD, SCRIP, scRNAtools, SPUTNIK, ssizeRNA, TransProR, TSGS
Suggests Me	ABSSeq, biobroom, ClassifyR, cqn, cydar, dcanr, dearseq, DEScan2, DiffBind, dittoSeq, DSS, easyreporting, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, GeoTcgaData, glmGamPoi, goseq, GSAR, GSVA, ideal, iSEEpathways, iSEEu, lemur, missMethyl, MoonlightR, multiMiR, raer, recount, regionReport, ribosomeProfilingQC, satuRn, scider, SeqGate, signifinder, SpliceWiz, stageR, subSeq, systemPipeR, TCGAbiolinks, tidybulk, topconfects, transmogR, tximeta, tximport, variancePartition, weitrix, Wrench, zenith, zFPKM, leeBamViews, CAGEWorkflow, chipseqDB, DGEobj, DGEobj.utils, DiPALM, easybio, glmmSeq, palasso, pctax, pmartR, seqgendiff, SIBERG, volcano3D
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	edgeR_4.5.6.tar.gz
Windows Binary (x86_64)	edgeR_4.5.6.zip
macOS Binary (x86_64)	edgeR_4.5.6.tgz
macOS Binary (arm64)	edgeR_4.5.6.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/
Package Downloads Report	Download Stats