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Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.1)

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   Reference Manual
Text   NEWS


biocViews ChIPSeq, DifferentialExpression, GeneExpression, RNASeq, SAGE, Sequencing, Software
Version 1.8.2
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
License LGPL (>= 3)
Depends S4Vectors, IRanges, GenomicRanges, Rcpp (>= 0.10.1), RcppArmadillo (>=
Imports BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, gplots, knitr, RColorBrewer, BiocStyle, airway, pasilla(>= 0.2.10), DESeq, vsn
Depends On Me DEXSeq, FourCSeq, MLSeq, rgsepd, TCC
Imports Me EnrichmentBrowser, FourCSeq, HTSFilter, phyloseq, ReportingTools, systemPipeR, ToPASeq
Suggests Me BiocGenerics, compcodeR, DiffBind, gage, oneChannelGUI
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