Package Recipe 'bioconductor-deseq2'

recipe bioconductor-deseq2¶

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.

Homepage: https://bioconductor.org/packages/3.9/bioc/html/DESeq2.html
License: LGPL (>= 3)
Recipe: /bioconductor-deseq2/meta.yaml
Links: biotools: deseq2, doi: 10.1186/s13059-014-0550-8

package bioconductor-deseq2¶

Versions: 1.22.1-0, 1.20.0-0, 1.18.1-1, 1.18.0-0, 1.16.1-3, 1.16.1-2, 1.16.1-0, 1.14.1-0, 1.12.4-5, 1.12.4-4, 1.12.4-3, 1.12.4-2, 1.12.4-1, 1.10.1-0, 1.10.0-1, 1.10.0-0, 1.8.2-0
Depends bioconductor-biobase: >=2.42.0,<2.43.0
Depends bioconductor-biocgenerics: >=0.28.0,<0.29.0
Depends bioconductor-biocparallel: >=1.16.0,<1.17.0
Depends bioconductor-genefilter: >=1.64.0,<1.65.0
Depends bioconductor-geneplotter: >=1.60.0,<1.61.0
Depends bioconductor-genomicranges: >=1.34.0,<1.35.0
Depends bioconductor-iranges: >=2.16.0,<2.17.0
Depends bioconductor-s4vectors: >=0.20.0,<0.21.0
Depends bioconductor-summarizedexperiment: >=1.12.0,<1.13.0
Depends libgcc-ng: >=7.3.0
Depends libstdcxx-ng: >=7.3.0
Depends r-base: >=3.5.1,<3.5.2.0a0
Depends r-ggplot2
Depends r-hmisc
Depends r-locfit
Depends r-rcpp: >=0.11.0
Depends r-rcpparmadillo
Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-deseq2

and update with:

conda update bioconductor-deseq2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-deseq2:<tag>

(see bioconductor-deseq2/tags for valid values for <tag>)

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-deseq2/README.html)