recipe bioconductor-cghcall

Calling aberrations for array CGH tumor profiles.

Homepage:

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

License:

GPL (http://www.gnu.org/copyleft/gpl.html)

Recipe:

/bioconductor-cghcall/meta.yaml

Links:

biotools: cghcall, doi: 10.1093/bioinformatics/btm030

Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.

package bioconductor-cghcall

(downloads) docker_bioconductor-cghcall

versions:
2.64.0-0,  2.62.0-0,  2.60.0-0,  2.56.0-0,  2.54.0-0,  2.52.0-1,  2.52.0-0,  2.50.0-0,  2.48.0-0, 

2.64.0-0,  2.62.0-0,  2.60.0-0,  2.56.0-0,  2.54.0-0,  2.52.0-1,  2.52.0-0,  2.50.0-0,  2.48.0-0,  2.46.0-1,  2.44.0-1,  2.44.0-0,  2.42.0-0,  2.40.0-0,  2.38.0-0,  2.34.1-0,  2.34.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-cghbase:

>=1.62.0,<1.63.0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0

depends bioconductor-impute:

>=1.76.0,<1.77.0

depends r-base:

>=4.3,<4.4.0a0

depends r-snowfall:

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-cghcall

and update with::

   mamba update bioconductor-cghcall

To create a new environment, run:

mamba create --name myenvname bioconductor-cghcall

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-cghcall:<tag>

(see `bioconductor-cghcall/tags`_ for valid values for ``<tag>``)

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Link to this page

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