edgeR

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see edgeR.

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: 3.16

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>

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

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")

edgeR Vignette PDF

edgeRUsersGuide.pdf PDF

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

Version 3.40.2

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 C++11

URL http://bioinf.wehi.edu.au/edgeR https://bioconductor.org/packages/edgeR

Suggests jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi, SummarizedExperiment, org.Hs.eg.db

Linking To Rcpp

Enhances

Depends On Me ASpli, EGSEA123, IntEREst, methylMnM, miloR, octad, 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, 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, ScreenR, SEtools, SIMD, SingleCellSignalR, singscore, SingscoreAMLMutations, sparrow, spatialHeatmap, spatialLIBD, 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, 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, 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_3.40.2.tar.gz

Windows Binary edgeR_3.40.2.zip (64-bit only)

macOS Binary (x86_64) edgeR_3.40.2.tgz

macOS Binary (arm64) edgeR_3.40.2.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

Old Source Packages for BioC 3.16 Source Archive