DESeq

DOI: 10.18129/B9.bioc.DESeq    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq.

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: 3.10

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 fs.tum.de>

Maintainer: Simon Anders <sanders at fs.tum.de>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DESeq")

 

PDF R Script Analysing RNA-Seq data with the "DESeq" package
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, DifferentialExpression, ImmunoOncology, RNASeq, SAGE, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 2.6 (R-2.11) (10 years)
License GPL (>= 3)
Depends BiocGenerics(>= 0.7.5), Biobase(>= 2.21.7), locfit, lattice
Imports genefilter, geneplotter, methods, MASS, RColorBrewer
LinkingTo
Suggests pasilla(>= 0.2.10), vsn, gplots
SystemRequirements
Enhances
URL http://www-huber.embl.de/users/anders/DESeq
Depends On Me DBChIP, EDDA, metaseqR, Polyfit, SeqGSEA, TCC, tRanslatome
Imports Me APAlyzer, ArrayExpressHTS, DEsubs, easyRNASeq, EDASeq, EDDA, gCMAP, HTSFilter, rnaSeqMap, scGPS, vulcan
Suggests Me BitSeq, compcodeR, dexus, DiffBind, ELBOW, gage, genefilter, IHWpaper, PROPER, regionReport, SSPA, ToPASeq, XBSeq
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DESeq_1.38.0.tar.gz
Windows Binary DESeq_1.38.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DESeq_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DESeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DESeq
Package Short Url https://bioconductor.org/packages/DESeq/
Package Downloads Report Download Stats

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