To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
In most cases, you don't need to download the package archive at all.
DESeq2
|
This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see DESeq2.
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: 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: Michael Love (HSPH Boston), Simon Anders, Wolfgang Huber (EMBL Heidelberg)
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
Citation (from within R,
enter citation("DESeq2")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DESeq2")
| R Script | Analyzing RNA-Seq data with the "DESeq2" package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, DifferentialExpression, GeneExpression, RNASeq, SAGE, Sequencing, Software |
| Version | 1.8.2 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | LGPL (>= 3) |
| Depends | S4Vectors, IRanges, GenomicRanges, Rcpp (>= 0.10.1), RcppArmadillo (>= 0.3.4.4) |
| Imports | BiocGenerics(>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc |
| LinkingTo | Rcpp, RcppArmadillo |
| Suggests | testthat, gplots, knitr, RColorBrewer, BiocStyle, airway, pasilla(>= 0.2.10), DESeq, vsn |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | DEXSeq, FourCSeq, MLSeq, rgsepd, TCC |
| Imports Me | EnrichmentBrowser, FourCSeq, HTSFilter, phyloseq, ReportingTools, systemPipeR, ToPASeq |
| Suggests Me | BiocGenerics, compcodeR, DiffBind, gage, oneChannelGUI |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DESeq2_1.8.2.tar.gz |
| Windows Binary | DESeq2_1.8.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DESeq2_1.8.2.tgz |
| Mac OS X 10.9 (Mavericks) | DESeq2_1.8.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DESeq2/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/DESeq2/ |
| 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
