DESeq2

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (2.14)

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 (HSPH Boston), Simon Anders, Wolfgang Huber (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 R Script Beginner's guide to the "DESeq2" package
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, DifferentialExpression, RNASeq, SAGE, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL (>= 3)
Depends GenomicRanges, IRanges, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4)
Imports BiocGenerics(>= 0.7.5), methods, locfit, genefilter, geneplotter, RColorBrewer, lattice
Suggests RUnit, gplots, knitr, Biobase, BiocStyle, parathyroidSE, pasilla(>= 0.2.10), DESeq, vsn, GenomicAlignments, GenomicFeatures, Rsamtools, biomaRt
System Requirements
URL
Depends On Me DEXSeq, MLSeq, TCC
Imports Me HTSFilter, phyloseq, ReportingTools
Suggests Me BiocGenerics, compcodeR, DiffBind, gage

Package Downloads

Package Source DESeq2_1.4.0.tar.gz
Windows Binary DESeq2_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DESeq2_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
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