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
|
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: 3.2
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")
| Analyzing RNA-seq data with the "DESeq2" package | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, DifferentialExpression, GeneExpression, RNASeq, SAGE, Sequencing, Software |
| Version | 1.10.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | LGPL (>= 3) |
| Depends | S4Vectors, IRanges, GenomicRanges, SummarizedExperiment(>= 0.2.0), 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, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, airway, pasilla(>= 0.2.10), DESeq |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | DEXSeq, FourCSeq, MLSeq, rgsepd, TCC, XBSeq |
| Imports Me | DChIPRep, EnrichmentBrowser, FourCSeq, HTSFilter, ReportingTools, SNPhood, systemPipeR, ToPASeq |
| Suggests Me | biobroom, BiocGenerics, compcodeR, DiffBind, gage, oneChannelGUI, phyloseq, subSeq |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DESeq2_1.10.1.tar.gz |
| Windows Binary | DESeq2_1.10.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DESeq2_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | DESeq2_1.10.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DESeq2/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/DESeq2/ |
| Package Downloads Report | Download Stats |
Documentation »
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