edgeR
Empirical analysis of digital gene expression data in R
Bioconductor version: Release (2.12)
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>, Aaron Lun <alun 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>
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
| R Script | edgeR Vignette | |
| edgeRUsersGuide.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bioinformatics, ChIPseq, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Software |
| Version | 3.2.4 |
| 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 |
| Imports Me | ArrayExpressHTS, DiffBind, HTSFilter, MEDIPS, Repitools, ReportingTools, rnaSeqMap, tweeDEseq |
| Suggests Me | baySeq, BitSeq, cqn, EDASeq, GenomicRanges, goseq, GSVA, leeBamViews, oneChannelGUI, pasilla, Repitools, SSPA |
Package Downloads
| Package Source | edgeR_3.2.4.tar.gz |
| Windows Binary | edgeR_3.2.4.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | edgeR_3.2.4.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: webmaster@bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2013
