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This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see DESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 3.2

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 Analyzing RNA-seq data with the "DESeq2" package
PDF   Reference Manual
Text   NEWS


biocViews ChIPSeq, DifferentialExpression, GeneExpression, RNASeq, SAGE, Sequencing, Software
Version 1.10.1
In Bioconductor since BioC 2.12 (R-3.0) (3 years)
License LGPL (>= 3)
Depends S4Vectors, IRanges, GenomicRanges, SummarizedExperiment(>= 0.2.0), Rcpp (>= 0.10.1), RcppArmadillo (>=
Imports BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, airway, pasilla(>= 0.2.10), DESeq
Depends On Me DEXSeq, FourCSeq, MLSeq, rgsepd, TCC, XBSeq
Imports Me DChIPRep, EnrichmentBrowser, FourCSeq, HTSFilter, ReportingTools, SNPhood, systemPipeR, ToPASeq
Suggests Me biobroom, BiocGenerics, compcodeR, DiffBind, gage, oneChannelGUI, phyloseq, subSeq
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