recipe bioconductor-pathifier

Quantify deregulation of pathways in cancer

Homepage:

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

License:

Artistic-1.0

Recipe:

/bioconductor-pathifier/meta.yaml

Links:

biotools: pathifier, doi: 10.1073/pnas.1219651110

Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

package bioconductor-pathifier

(downloads) docker_bioconductor-pathifier

versions:
1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0, 

1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.16.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-princurve:

>=2.0.4

depends r-r.oo:

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-pathifier

and update with::

   mamba update bioconductor-pathifier

To create a new environment, run:

mamba create --name myenvname bioconductor-pathifier

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-pathifier:<tag>

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