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

   

This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see edgeR.

Empirical analysis of digital gene expression data in R

Bioconductor version: 2.10

Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data.

Author: Mark Robinson <mrobinson at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Yunshun Chen <yuchen at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>

Maintainer: Mark Robinson <mrobinson at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Yunshun Chen <yuchen 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 Bioinformatics, ChIPseq, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Software
Version 2.6.12
In Bioconductor since BioC 2.3 (R-2.8) (7.5 years)
License LGPL (>= 2)
Depends R (>= 2.3.0), methods, limma
Imports
LinkingTo
Suggests MASS, statmod, splines
SystemRequirements
Enhances
URL
Depends On Me easyRNASeq, manta
Imports Me ArrayExpressHTS, DiffBind, Repitools, rnaSeqMap, tweeDEseq
Suggests Me baySeq, cqn, EDASeq, GenomicRanges, goseq, GSVA, leeBamViews, oneChannelGUI, pasilla, Repitools
Build Report  

Package Archives

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

Package Source edgeR_2.6.12.tar.gz
Windows Binary edgeR_2.6.12.zip
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/edgeR/tree/release-2.10
Package Short Url http://bioconductor.org/packages/edgeR/
Package Downloads Report Download Stats

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