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Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 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>

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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


biocViews ChIPSeq, DifferentialExpression, RNASeq, SAGE, Sequencing, Software
Version 1.4.5
In Bioconductor since BioC 2.12 (R-3.0)
License GPL (>= 3)
Depends GenomicRanges, IRanges, Rcpp (>= 0.10.1), RcppArmadillo (>=
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
Depends On Me DEXSeq, MLSeq, TCC
Imports Me HTSFilter, phyloseq, ReportingTools
Suggests Me BiocGenerics, compcodeR, DiffBind, gage

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