recipe bioconductor-pathlinkr

Analyze and interpret RNA-Seq results

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-pathlinkr/meta.yaml

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

package bioconductor-pathlinkr

(downloads) docker_bioconductor-pathlinkr

versions:

requirements:

additional platforms:

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-pathlinkr

and update with::

   mamba update bioconductor-pathlinkr

To create a new environment, run:

mamba create --name myenvname bioconductor-pathlinkr

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-pathlinkr:<tag>

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