recipe bioconductor-terratcgadata

OpenAccess TCGA Data on Terra as MultiAssayExperiment

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-terratcgadata/meta.yaml

Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.

package bioconductor-terratcgadata

versions:

1.4.0-0,  1.2.0-0

depends bioconductor-anvil:

>=1.12.0,<1.13.0

depends bioconductor-biocfilecache:

>=2.8.0,<2.9.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-multiassayexperiment:

>=1.26.0,<1.27.0

depends bioconductor-raggedexperiment:

>=1.24.0,<1.25.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-tcgautils:

>=1.20.0,<1.21.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-readr:

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-terratcgadata

and update with::

   mamba update bioconductor-terratcgadata

To create a new environment, run:

mamba create --name myenvname bioconductor-terratcgadata

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-terratcgadata:<tag>

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

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