recipe bioconductor-cnvranger

Summarization and expression/phenotype association of CNV ranges

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/CNVRanger.html

License:

Artistic-2.0

Recipe:

/bioconductor-cnvranger/meta.yaml

The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.

package bioconductor-cnvranger

versions:

1.16.4-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-edger:

>=3.42.0,<3.43.0

depends bioconductor-gdsarray:

>=1.20.0,<1.21.0

depends bioconductor-gdsfmt:

>=1.36.0,<1.37.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends bioconductor-raggedexperiment:

>=1.24.0,<1.25.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-snprelate:

>=1.34.0,<1.35.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-lattice:

depends r-plyr:

depends r-qqman:

depends r-rappdirs:

depends r-reshape2:

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-cnvranger

and update with::

   mamba update bioconductor-cnvranger

To create a new environment, run:

mamba create --name myenvname bioconductor-cnvranger

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-cnvranger:<tag>

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

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