To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")

In most cases, you don't need to download the package archive at all.

edgeR

DOI: 10.18129/B9.bioc.edgeR

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor version: Release (3.5)

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 counts, including ChIP-seq, SAGE and CAGE.

Author: Yunshun Chen <yuchen at wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Xiaobei Zhou <xiaobei.zhou at uzh.ch>, Mark Robinson <mark.robinson at imls.uzh.ch>, Gordon Smyth <smyth at wehi.edu.au>

Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Mark Robinson <mark.robinson at imls.uzh.ch>, Davis McCarthy <dmccarthy at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")

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, ChIPSeq, Clustering, Coverage, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, Genetics, MultipleComparison, Normalization, QualityControl, RNASeq, Regression, SAGE, Sequencing, Software, TimeCourse, Transcription
Version	3.18.1
In Bioconductor since	BioC 2.3 (R-2.8) (9 years)
License	GPL (>=2)
Depends	R (>= 2.15.0), limma
Imports	graphics, stats, utils, methods, locfit
LinkingTo
Suggests	MASS, statmod, splines, KernSmooth
SystemRequirements
Enhances
URL	http://bioinf.wehi.edu.au/edgeR
Depends On Me	DBChIP, EDDA, IntEREst, manta, methylMnM, MLSeq, RnaSeqGeneEdgeRQL, RnaSeqSampleSizeData, RUVSeq, samExploreR, TCC, tRanslatome
Imports Me	affycoretools, ampliQueso, ArrayExpressHTS, ASpli, baySeq, compcodeR, coseq, csaw, debrowser, DEFormats, DEGreport, DEsubs, DiffBind, diffHic, diffloop, DRIMSeq, easyRNASeq, EBSEA, EDDA, eegc, EGSEA, EnrichmentBrowser, erccdashboard, Glimma, HTSFilter, MEDIPS, metaseqR, MIGSA, msgbsR, msmsTests, PathoStat, PROPER, PureCN, regsplice, Repitools, ReportingTools, rnaSeqMap, RnaSeqSampleSize, scater, scde, scone, scran, splatter, STATegRa, SVAPLSseq, systemPipeR, TCGAbiolinks, TCseq, ToPASeq, tweeDEseq, yarn
Suggests Me	ABSSeq, biobroom, BitSeq, ClassifyR, clonotypeR, cqn, cydar, EDASeq, gage, gCrisprTools, GenomicAlignments, GenomicRanges, goseq, groHMM, GSAR, GSVA, ideal, JctSeqData, leeBamViews, missMethyl, oneChannelGUI, regionReport, SSPA, subSeq, tximport, variancePartition
Build Report

Package Archives

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

Source Package	edgeR_3.18.1.tar.gz
Windows Binary	edgeR_3.18.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	edgeR_3.18.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/edgeR
Package Short Url	http://bioconductor.org/packages/edgeR/
Package Downloads Report	Download Stats

Documentation »

Bioconductor

Package vignettes and manuals.
Workflows for learning and use.
Course and conference material.
Videos.
Community resources and tutorials.

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Support site - for questions about Bioconductor packages
Bioc-devel mailing list - for package developers