Differential gene expression analysis based on the negative binomial distribution

 

DESeq2

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Development (2.12)

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution

Author: Michael Love (MPIMG Berlin), Simon Anders (EMBL Heidelberg)

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("DESeq2")

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

    citation("DESeq2")

Documentation

PDF	R Script	Analyzing RNA-Seq data with the "DESeq2" package
PDF		vst.pdf
PDF		Reference Manual

Details

biocViews	ChIPseq, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Software
Version	0.99.18
In Bioconductor since	BioC 2.12 (R-2.16)
License	GPL (>= 3)
Depends	GenomicRanges, IRanges, Biobase, lattice, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4)
Imports	GenomicRanges, IRanges, Biobase, locfit, genefilter, methods, RColorBrewer, lattice
Suggests	parathyroidSE, pasilla(>= 0.2.10), vsn, gplots
System Requirements
URL
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Imports Me
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Package Downloads

Package Source	DESeq2_0.99.18.tar.gz
Windows Binary	DESeq2_0.99.18.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	DESeq2_0.99.18.tgz