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Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.4)

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, Simon Anders, Wolfgang Huber

Maintainer: Michael Love <michaelisaiahlove at>

Citation (from within R, enter citation("DESeq2")):


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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, Transcription
Version 1.14.0
In Bioconductor since BioC 2.12 (R-3.0) (3.5 years)
License LGPL (>= 3)
Depends S4Vectors(>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment(>= 1.1.6)
Imports BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, airway, IHW, tximport, tximportData, readr, pasilla(>= 0.2.10)
Depends On Me ASpli, DChIPRep, DEXSeq, FourCSeq, MLSeq, rgsepd, TCC, XBSeq
Imports Me anamiR, debrowser, DEFormats, DEsubs, DiffBind, eegc, EnrichmentBrowser, FourCSeq, GenoGAM, Glimma, HTSFilter, IHWpaper, isomiRs, JunctionSeq, pcaExplorer, regionReport, ReportingTools, SNPhood, systemPipeR, ToPASeq
Suggests Me biobroom, BiocGenerics, compcodeR, DEGreport, derfinder, gage, GenomicAlignments, GenomicRanges, IHW, JctSeqData, oneChannelGUI, phyloseq, recount, RUVSeq, scran, Single.mTEC.Transcriptomes, subSeq, tximport, variancePartition
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