recipe bioconductor-spia

Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-spia/meta.yaml

Links:

biotools: spia, doi: 10.1093/bioinformatics/btn577

This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.

package bioconductor-spia

(downloads) docker_bioconductor-spia

versions:
2.58.0-0,  2.54.0-0,  2.52.0-0,  2.50.0-0,  2.46.0-0,  2.44.0-0,  2.42.0-1,  2.42.0-0,  2.40.0-0, 

2.58.0-0,  2.54.0-0,  2.52.0-0,  2.50.0-0,  2.46.0-0,  2.44.0-0,  2.42.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-0,  2.36.0-1,  2.34.0-0,  2.32.0-0,  2.30.0-0,  2.28.0-0

depends bioconductor-kegggraph:

>=1.66.0,<1.67.0

depends r-base:

>=4.4,<4.5.0a0

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-spia

and update with::

   mamba update bioconductor-spia

To create a new environment, run:

mamba create --name myenvname bioconductor-spia

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-spia:<tag>

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