recipe bioconductor-cnanorm

A normalization method for Copy Number Aberration in cancer samples

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-cnanorm/meta.yaml

Links:

biotools: cnanorm

Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.

package bioconductor-cnanorm

(downloads) docker_bioconductor-cnanorm

versions:
1.48.0-0,  1.46.1-0,  1.44.0-1,  1.44.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-1, 

1.48.0-0,  1.46.1-0,  1.44.0-1,  1.44.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.1-0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends libgfortran-ng:

depends libgfortran5:

>=12.3.0

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-cnanorm

and update with::

   mamba update bioconductor-cnanorm

To create a new environment, run:

mamba create --name myenvname bioconductor-cnanorm

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-cnanorm:<tag>

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