To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq")
In most cases, you don't need to download the package archive at all.
DESeq
|
|
|
|
|
|
|
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: Release (3.1)
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 and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DESeq")
| R Script | Analysing RNA-Seq data with the "DESeq" package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, DifferentialExpression, RNASeq, SAGE, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (5.5 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 | ampliQueso, ArrayExpressHTS, easyRNASeq, EDASeq, EDDA, gCMAP, HTSFilter, rnaSeqMap, ToPASeq |
| Suggests Me | BitSeq, compcodeR, DESeq2, dexus, DiffBind, ELBOW, gage, genefilter, GenomicAlignments, GenomicRanges, oneChannelGUI, pasilla, PROPER, RUVSeq, SSPA |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DESeq_1.20.0.tar.gz |
| Windows Binary | DESeq_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DESeq_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | DESeq_1.20.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DESeq/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/DESeq/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
