recipe bioconductor-pcxn

Exploring, analyzing and visualizing functions utilizing the pcxnData package

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/pcxn.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-pcxn/meta.yaml

Discover the correlated pathways/gene sets of a single pathway/gene set or discover correlation relationships among multiple pathways/gene sets. Draw a heatmap or create a network of your query and extract members of each pathway/gene set found in the available collections (MSigDB H hallmark, MSigDB C2 Canonical pathways, MSigDB C5 GO BP and Pathprint).

package bioconductor-pcxn

(downloads) docker_bioconductor-pcxn

versions:
2.24.0-0,  2.22.0-0,  2.20.0-0,  2.16.0-0,  2.14.0-0,  2.12.0-2,  2.12.0-0,  2.10.0-0,  2.8.0-1, 

2.24.0-0,  2.22.0-0,  2.20.0-0,  2.16.0-0,  2.14.0-0,  2.12.0-2,  2.12.0-0,  2.10.0-0,  2.8.0-1,  2.6.0-1,  2.6.0-0,  2.4.0-0

depends bioconductor-pcxndata:

>=2.24.0,<2.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-pheatmap:

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-pcxn

and update with::

   mamba update bioconductor-pcxn

To create a new environment, run:

mamba create --name myenvname bioconductor-pcxn

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-pcxn:<tag>

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

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Link to this page

Render an install-with-bioconda 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-pcxn/README.html)