recipe bioconductor-pcxndata

Correlation coefficients and p values between pre-defined pathway/gene sets

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/pcxnData.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-pcxndata/meta.yaml

PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs.

package bioconductor-pcxndata

(downloads) docker_bioconductor-pcxndata

versions:
2.24.0-0,  2.22.0-0,  2.19.0-0,  2.16.0-1,  2.16.0-0,  2.14.0-0,  2.12.0-2,  2.12.0-1,  2.12.0-0, 

2.24.0-0,  2.22.0-0,  2.19.0-0,  2.16.0-1,  2.16.0-0,  2.14.0-0,  2.12.0-2,  2.12.0-1,  2.12.0-0,  2.11.0-0,  2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.4.0-0

depends bioconductor-data-packages:

>=20231203

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-pcxndata

and update with::

   mamba update bioconductor-pcxndata

To create a new environment, run:

mamba create --name myenvname bioconductor-pcxndata

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-pcxndata:<tag>

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

Download stats

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-pcxndata/README.html)