recipe bioconductor-cbaf

Automated functions for comparing various omic data from cbioportal.org

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-cbaf/meta.yaml

This package contains functions that allow analysing and comparing omic data across various cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.

package bioconductor-cbaf

(downloads) docker_bioconductor-cbaf

versions:
1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.12.0-0,  1.8.0-0, 

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.12.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

depends bioconductor-biocfilecache:

>=2.14.0,<2.15.0

depends bioconductor-cbioportaldata:

>=2.18.0,<2.19.0

depends bioconductor-genefilter:

>=1.88.0,<1.89.0

depends r-base:

>=4.4,<4.5.0a0

depends r-gplots:

depends r-openxlsx:

depends r-rcolorbrewer:

depends r-zip:

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-cbaf

and update with::

   mamba update bioconductor-cbaf

To create a new environment, run:

mamba create --name myenvname bioconductor-cbaf

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-cbaf:<tag>

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