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This is the development version of DESeq2; for the stable release version, see DESeq2.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Development (3.3)

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 1.11.2
In Bioconductor since BioC 2.12 (R-3.0) (2.5 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, derfinder, DiffBind, gage, oneChannelGUI, phyloseq, subSeq
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