recipe bioconductor-conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-conumee/meta.yaml

This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.

package bioconductor-conumee

versions:

1.32.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1

depends bioconductor-dnacopy:

>=1.72.0,<1.73.0

depends bioconductor-genomeinfodb:

>=1.34.0,<1.35.0

depends bioconductor-genomicranges:

>=1.50.0,<1.51.0

depends bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19:

>=0.6.0,<0.7.0

depends bioconductor-illuminahumanmethylation450kmanifest:

>=0.4.0,<0.5.0

depends bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19:

>=0.6.0,<0.7.0

depends bioconductor-illuminahumanmethylationepicmanifest:

>=0.3.0,<0.4.0

depends bioconductor-iranges:

>=2.32.0,<2.33.0

depends bioconductor-minfi:

>=1.44.0,<1.45.0

depends bioconductor-rtracklayer:

>=1.58.0,<1.59.0

depends r-base:

>=4.2,<4.3.0a0

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-conumee

and update with::

   mamba update bioconductor-conumee

To create a new environment, run:

mamba create --name myenvname bioconductor-conumee

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-conumee:<tag>

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

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