recipe bioconductor-reactomepa

Reactome Pathway Analysis

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/ReactomePA.html

License:

GPL-2

Recipe:

/bioconductor-reactomepa/meta.yaml

Links:

biotools: reactomepa

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.

package bioconductor-reactomepa

versions:

1.44.0-0,  1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1, 

1.44.0-0,  1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-dose:

>=3.26.0,<3.27.0

depends bioconductor-enrichplot:

>=1.20.0,<1.21.0

depends bioconductor-graphite:

>=1.46.0,<1.47.0

depends bioconductor-reactome.db:

>=1.84.0,<1.85.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

>=3.3.5

depends r-ggraph:

depends r-gson:

depends r-igraph:

requirements:

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-reactomepa

and update with::

   mamba update bioconductor-reactomepa

To create a new environment, run:

mamba create --name myenvname bioconductor-reactomepa

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-reactomepa:<tag>

(see `bioconductor-reactomepa/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-reactomepa/README.html)