recipe bioconductor-copa

Functions to perform cancer outlier profile analysis.

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-copa/meta.yaml

Links:

biotools: copa, usegalaxy-eu: copa

COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.

package bioconductor-copa

(downloads) docker_bioconductor-copa

versions:
1.70.0-1,  1.70.0-0,  1.68.0-0,  1.66.0-1,  1.66.0-0,  1.62.0-2,  1.62.0-1,  1.62.0-0,  1.60.0-0, 

1.70.0-1,  1.70.0-0,  1.68.0-0,  1.66.0-1,  1.66.0-0,  1.62.0-2,  1.62.0-1,  1.62.0-0,  1.60.0-0,  1.58.0-1,  1.58.0-0,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.50.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

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-copa

and update with::

   mamba update bioconductor-copa

To create a new environment, run:

mamba create --name myenvname bioconductor-copa

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-copa:<tag>

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