edgeR

Empirical analysis of digital gene expression data in R

Bioconductor version: Release (2.7)

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, Davis McCarthy , Gordon Smyth

Maintainer: Mark Robinson , Davis McCarthy , Gordon Smyth

To install this package, start R and enter:

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

Documentation

PDF	R Script	edgeR User's Guide
PDF		edgeR_case_study_Li_MDSplot.pdf
PDF		edgeR_case_study_longSAGE_MDSplot.pdf

Reference Manual

Details

biocViews	Bioinformatics, DifferentialExpression, SAGE, HighThroughputSequencing, RNAseq
Depends	R, methods
Imports	limma
Suggests	MASS
System Requirements
License	LGPL (>= 2)
URL
Depends On Me	oneChannelGUI
Imports Me	rnaSeqMap
Suggests Me	goseq
Version	2.0.5

Package Downloads

Package Source	edgeR_2.0.5.tar.gz
Windows Binary	edgeR_2.0.5.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	edgeR_2.0.5.tgz
Package Downloads Report	Download Stats