DESeq

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see DESeq (See replacement DESeq2).

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

Details

biocViews ChIPSeq, DifferentialExpression, ImmunoOncology, RNASeq, SAGE, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 2.6 (R-2.11) (14 years)
License GPL (>= 3)
Depends BiocGenerics(>= 0.7.5), Biobase(>= 2.21.7), locfit, lattice
Imports genefilter, geneplotter, methods, MASS, RColorBrewer
System Requirements
URL http://www-huber.embl.de/users/anders/DESeq
See More
Suggests pasilla(>= 0.2.10), vsn, gplots
Linking To
Enhances
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 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
Bioc Package Browser https://code.bioconductor.org/browse/DESeq/
Package Short Url https://bioconductor.org/packages/DESeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive