edgeR (original) (raw)
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, seeedgeR.
Empirical analysis of digital gene expression data in R
Bioconductor version: 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 , Davis McCarthy , Yunshun Chen , Aaron Lun , Gordon Smyth
Maintainer: Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
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 | 3.2.4 |
| 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 |
| Imports Me | ArrayExpressHTS, DiffBind, HTSFilter, MEDIPS, Repitools, ReportingTools, rnaSeqMap, tweeDEseq |
| Suggests Me | baySeq, BitSeq, cqn, EDASeq, GenomicRanges, goseq, GSVA, leeBamViews, oneChannelGUI, pasilla, Repitools, SSPA |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| 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 |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/edgeR/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/edgeR/ |
| Package Downloads Report | Download Stats |