recipe bioconductor-cnvrd2

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/CNVrd2.html

License:

GPL-2

Recipe:

/bioconductor-cnvrd2/meta.yaml

CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

package bioconductor-cnvrd2

(downloads) docker_bioconductor-cnvrd2

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,  1.20.0-0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-gridextra:

depends r-rjags:

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-cnvrd2

and update with::

   mamba update bioconductor-cnvrd2

To create a new environment, run:

mamba create --name myenvname bioconductor-cnvrd2

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-cnvrd2:<tag>

(see `bioconductor-cnvrd2/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-cnvrd2/README.html)