recipe bioconductor-rtcga.cnv

CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/RTCGA.CNV.html

License:

GPL-2

Recipe:

/bioconductor-rtcga.cnv/meta.yaml

Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot.

package bioconductor-rtcga.cnv

(downloads) docker_bioconductor-rtcga.cnv

versions:
1.30.0-0,  1.28.0-0,  1.25.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0, 

1.30.0-0,  1.28.0-0,  1.25.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-rtcga:

>=1.32.0,<1.33.0

depends curl:

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-rtcga.cnv

and update with::

   mamba update bioconductor-rtcga.cnv

To create a new environment, run:

mamba create --name myenvname bioconductor-rtcga.cnv

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-rtcga.cnv:<tag>

(see `bioconductor-rtcga.cnv/tags`_ for valid values for ``<tag>``)

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