recipe bioconductor-deseq2

Differential gene expression analysis based on the negative binomial distribution

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/DESeq2.html

License:

LGPL (>= 3)

Recipe:

/bioconductor-deseq2/meta.yaml

Links:

biotools: deseq2, doi: 10.1186/s13059-014-0550-8, usegalaxy-eu: 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.

package bioconductor-deseq2

versions:

1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.2-0,  1.38.0-1,  1.38.0-0,  1.34.0-3, 

1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.2-0,  1.38.0-1,  1.38.0-0,  1.34.0-3,  1.34.0-2,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.1-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  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:

>=2.66.0,<2.67.0

depends bioconductor-biobase:

>=2.66.0,<2.67.0a0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0a0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0a0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0a0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

>=3.4.0

depends r-locfit:

depends r-matrixstats:

depends r-rcpp:

>=0.11.0

depends r-rcpparmadillo:

requirements:

additional platforms:

linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-deseq2

and update with::

   mamba update bioconductor-deseq2

To create a new environment, run:

mamba create --name myenvname bioconductor-deseq2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

Download stats

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)