recipe bioconductor-progeny

Pathway RespOnsive GENes for activity inference from gene expression

Homepage:

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

License:

Apache License (== 2.0) | file LICENSE

Recipe:

/bioconductor-progeny/meta.yaml

PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.

package bioconductor-progeny

(downloads) docker_bioconductor-progeny

versions:
1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1, 

1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.1-0,  1.4.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-decoupler:

>=2.6.0,<2.7.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-gridextra:

depends r-reshape2:

depends r-tidyr:

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-progeny

and update with::

   mamba update bioconductor-progeny

To create a new environment, run:

mamba create --name myenvname bioconductor-progeny

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-progeny:<tag>

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