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 2.13 of Bioconductor; for the stable, up-to-date release version, see 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>
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")
| R Script | edgeR Vignette | |
| edgeRUsersGuide.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) (7.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 2.15.0), methods, limma |
| Imports | |
| LinkingTo | |
| Suggests | MASS, statmod, splines, locfit, KernSmooth |
| SystemRequirements | |
| Enhances | |
| 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 |
| Build Report |
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 |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/edgeR/tree/release-2.13 |
| Package Short Url | http://bioconductor.org/packages/edgeR/ |
| Package Downloads Report | Download Stats |
Documentation »
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