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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 (3.19)

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")):

Installation

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

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 4.1.17
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
See More
Suggests jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject
Linking To Rcpp
Enhances
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, 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, MIRit, MLSeq, moanin, mobileRNA, MOSim, Motif2Site, msgbsR, msmsTests, multiHiCcompare, muscat, PathoStat, phantasus, PhIPData, ppcseq, PROPER, psichomics, RCM, recountWorkflow, regsplice, Repitools, ReportingTools, RNAseqCovarImpute, RnaSeqSampleSize, ROSeq, Rvisdiff, saseR, scCB2, scde, scone, scran, ScreenR, SEtools, SIMD, SingleCellSignalR, singscore, SingscoreAMLMutations, sparrow, spatialHeatmap, spatialLIBD, speckle, splatter, SPsimSeq, srnadiff, sSNAPPY, standR, STATegRa, SurfR, sva, TBSignatureProfiler, TCseq, tradeSeq, treekoR, tweeDEseq, vidger, xcore, yarn, zinbwave
Suggests Me ABSSeq, 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
Links To Me
Build Report Build Report

Package Archives

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

Source Package edgeR_4.1.17.tar.gz
Windows Binary edgeR_4.1.17.zip (64-bit only)
macOS Binary (x86_64) edgeR_4.1.17.tgz
macOS Binary (arm64) edgeR_4.1.17.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