DESeq

DOI: 10.18129/B9.bioc.DESeq    

Differential gene expression analysis based on the negative binomial distribution

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") 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	1.39.0
In Bioconductor since	BioC 2.6 (R-2.11) (10.5 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, metaseqR2, 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_1.39.0.tar.gz
Windows Binary	DESeq_1.39.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
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