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("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 | R Script | |
| Reference Manual | ||
| 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 |