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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: Simon Anders, EMBL Heidelberg <sanders at>

Maintainer: Simon Anders <sanders at>

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PDF R Script Analysing RNA-Seq data with the "DESeq" package
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biocViews ChIPSeq, DifferentialExpression, RNASeq, SAGE, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 2.6 (R-2.11)
License GPL (>= 3)
Depends BiocGenerics(>= 0.7.5), Biobase(>= 2.21.7), locfit, lattice
Imports genefilter, geneplotter, methods, MASS, RColorBrewer
Suggests pasilla(>= 0.2.10), vsn, gplots
System Requirements
Depends On Me DBChIP, EDDA, metaseqR, parathyroid, SeqGSEA, TCC, tRanslatome
Imports Me ampliQueso, ArrayExpressHTS, easyRNASeq, EDASeq, EDDA, HTSFilter, rnaSeqMap
Suggests Me BitSeq, compcodeR, DESeq2, dexus, DiffBind, EDASeq, ELBOW, gage, gCMAP, genefilter, GenomicAlignments, GenomicRanges, oneChannelGUI, pasilla, SSPA

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