edgeR

Empirical analysis of digital gene expression data in R

Bioconductor version: Release (2.14)

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

Maintainer: Yunshun Chen <yuchen 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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("edgeR")

Documentation

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

Details

biocViews Bioinformatics, ChIPseq, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Software
Version 3.6.0
In Bioconductor since BioC 2.3 (R-2.8)
License GPL (>=2)
Depends R (>= 2.15.0), limma
Imports methods
Suggests MASS, statmod, splines, locfit, KernSmooth
System Requirements
URL
Depends On Me DBChIP, EDDA, manta, methylMnM, MLSeq, TCC, tRanslatome
Imports Me ampliQueso, ArrayExpressHTS, compcodeR, DiffBind, DSS, easyRNASeq, EDDA, HTSFilter, MEDIPS, metaseqR, msmsTests, Repitools, ReportingTools, rnaSeqMap, tweeDEseq
Suggests Me baySeq, BitSeq, clonotypeR, cqn, EDASeq, gage, GenomicAlignments, GenomicRanges, goseq, GSVA, leeBamViews, oneChannelGUI, pasilla, SSPA

Package Downloads

Package Source edgeR_3.6.0.tar.gz
Windows Binary edgeR_3.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) edgeR_3.6.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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