source("http://bioconductor.org/biocLite.R")
biocLite("edgeR")

edgeR

Empirical analysis of digital gene expression data in R

Bioconductor version: 2.13

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

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

Installation

To install this package, start R and enter:

source("http://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	R Script	edgeR Vignette
PDF		edgeRUsersGuide.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bioinformatics, ChIPseq, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Software
Version	3.4.2
In Bioconductor since	BioC 2.3 (R-2.8)
License	GPL (>=2)
Depends	R (>= 2.15.0), methods, limma
Imports
Suggests	MASS, statmod, splines, locfit, KernSmooth
System Requirements
URL
Depends On Me	DBChIP, easyRNASeq, manta, methylMnM, TCC, tRanslatome
Imports Me	ampliQueso, ArrayExpressHTS, DiffBind, DSS, HTSFilter, MEDIPS, msmsTests, Repitools, ReportingTools, rnaSeqMap, tweeDEseq
Suggests Me	baySeq, BitSeq, clonotypeR, cqn, EDASeq, gage, GenomicRanges, goseq, GSVA, leeBamViews, oneChannelGUI, pasilla, SSPA

Package Archives

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

Package Source	edgeR_3.4.2.tar.gz
Windows Binary	edgeR_3.4.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	edgeR_3.4.2.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats