edgeR

DOI: 10.18129/B9.bioc.edgeR    

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: Release (3.15)

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, 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>

Installation

To install this package, start R (version "4.2") 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")

 

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

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, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Version	3.38.4
In Bioconductor since	BioC 2.3 (R-2.8) (14 years)
License	GPL (>=2)
Depends	R (>= 3.6.0), limma(>= 3.41.5)
Imports	methods, graphics, stats, utils, locfit, Rcpp
LinkingTo	Rcpp
Suggests	jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi, SummarizedExperiment, org.Hs.eg.db
SystemRequirements	C++11
Enhances
URL	http://bioinf.wehi.edu.au/edgeR https://bioconductor.org/packages/edgeR
Depends On Me	ASpli, EGSEA123, IntEREst, methylMnM, miloR, ReactomeGSA.data, RNAseq123, rnaseqDTU, RnaSeqGeneEdgeRQL, RNASeqR, RnaSeqSampleSizeData, RUVSeq, TCC, tRanslatome
Imports Me	affycoretools, anota2seq, ArrayExpressHTS, ATACseqQC, autonomics, AWFisher, baySeq, beer, benchdamic, BioQC, censcyt, ChromSCape, circRNAprofiler, clusterExperiment, CNVRanger, compcodeR, consensusDE, coseq, countsimQC, crossmeta, csaw, DaMiRseq, dce, debrowser, DEComplexDisease, DEFormats, DEGreport, DEsubs, diffcyt, diffHic, diffloop, diffUTR, DMRcate, doseR, DRIMSeq, DropletUtils, easyRNASeq, eegc, EGSEA, eisaR, emtdata, EnrichmentBrowser, erccdashboard, ERSSA, ExpHunterSuite, extraChIPs, GDCRNATools, Glimma, GSEABenchmarkeR, hermes, HTSFilter, icetea, infercnv, IsoformSwitchAnalyzeR, KnowSeq, Maaslin2, MEDIPS, metaseqR2, microbiomeMarker, MIGSA, MLSeq, moanin, Motif2Site, msgbsR, msmsTests, multiHiCcompare, muscat, NBSplice, PathoStat, PhIPData, ppcseq, PROPER, psichomics, RCM, recountWorkflow, regsplice, Repitools, ReportingTools, RnaSeqSampleSize, ROSeq, scCB2, scde, scone, scran, SEtools, SIMD, SingleCellSignalR, singscore, SingscoreAMLMutations, sparrow, spatialHeatmap, splatter, SPsimSeq, srnadiff, sSNAPPY, standR, STATegRa, sva, TBSignatureProfiler, TCseq, TimeSeriesExperiment, tradeSeq, treekoR, tweeDEseq, vidger, xcore, yarn, zinbwave
Suggests Me	ABSSeq, bigPint, biobroom, CAGEWorkflow, chipseqDB, ClassifyR, clonotypeR, cqn, cydar, dcanr, dearseq, DEScan2, dittoSeq, easyreporting, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, glmGamPoi, goseq, groHMM, GSAR, GSVA, ideal, iSEEu, leeBamViews, missMethyl, multiMiR, recount, regionReport, ribosomeProfilingQC, satuRn, SeqGate, stageR, subSeq, SummarizedBenchmark, systemPipeR, TCGAbiolinks, tidybulk, topconfects, tximeta, tximport, variancePartition, weitrix, Wrench, zFPKM
Links To Me
Build Report

Package Archives

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

Source Package	edgeR_3.38.4.tar.gz
Windows Binary	edgeR_3.38.4.zip (64-bit only)
macOS Binary (x86_64)	edgeR_3.38.4.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
Old Source Packages for BioC 3.15	Source Archive