edgeR

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: Release (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 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 "4.4") and enter:


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

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, QualityControl, RNASeq, Regression, SAGE, Sequencing, SingleCell, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version	4.4.0
In Bioconductor since	BioC 2.3 (R-2.8) (16 years)
License	GPL (>=2)
Depends	R (>= 3.6.0), limma(>= 3.61.9)
Imports	methods, graphics, stats, utils, locfit
System Requirements
URL	https://bioinf.wehi.edu.au/edgeR/ https://bioconductor.org/packages/edgeR

Suggests	jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject
Linking To
Enhances
Depends On Me	ASpli, IntEREst, methylMnM, miloR, octad, RUVSeq, TCC, tRanslatome, ReactomeGSA.data, EGSEA123, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, csawBook, OSCA.workflows, babel, BALLI, BioInsight, SCdeconR
Imports Me	affycoretools, ATACseqQC, autonomics, AWFisher, baySeq, beer, BioQC, broadSeq, censcyt, ChromSCape, circRNAprofiler, CleanUpRNAseq, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, csaw, cypress, DaMiRseq, Damsel, dce, debrowser, DEFormats, DEGreport, DESpace, DEsubs, diffcyt, diffHic, diffUTR, 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, IsoformSwitchAnalyzeR, KnowSeq, 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, saseR, scCB2, scde, scone, scran, ScreenR, SEtools, SIMD, SingleCellSignalR, singscore, SpaNorm, sparrow, spatialHeatmap, speckle, splatter, SPsimSeq, sSNAPPY, standR, STATegRa, sva, TCseq, tradeSeq, treeclimbR, treekoR, tweeDEseq, vidger, xcore, yarn, zinbwave, emtdata, spatialLIBD, ExpHunterSuite, recountWorkflow, SingscoreAMLMutations, aIc, bulkAnalyseR, CAMML, cinaR, CoreMicrobiomeR, ggpicrust2, HTSCluster, MetaLonDA, microbial, 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, 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, easybio, glmmSeq, MiscMetabar, 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_4.4.0.tar.gz
Windows Binary (x86_64)	edgeR_4.4.0.zip
macOS Binary (x86_64)	edgeR_4.4.0.tgz
macOS Binary (arm64)	edgeR_4.4.0.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