recipe bioconductor-cbioportaldata

Exposes and makes available data from the cBioPortal web resources

Homepage:

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

License:

AGPL-3

Recipe:

/bioconductor-cbioportaldata/meta.yaml

The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.

package bioconductor-cbioportaldata

versions:

2.14.0-0,  2.12.0-0,  2.10.0-0,  2.6.0-0,  2.4.0-0,  2.2.8-0,  2.2.3-0,  2.0.3-0

depends bioconductor-anvil:

>=1.14.0,<1.15.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-raggedexperiment:

>=1.26.0,<1.27.0

depends bioconductor-rtcgatoolbox:

>=2.32.0,<2.33.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-tcgautils:

>=1.22.0,<1.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-digest:

depends r-dplyr:

depends r-httr:

depends r-readr:

depends r-tibble:

depends r-tidyr:

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-cbioportaldata

and update with::

   mamba update bioconductor-cbioportaldata

To create a new environment, run:

mamba create --name myenvname bioconductor-cbioportaldata

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-cbioportaldata:<tag>

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

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Link to this page

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