recipe bioconductor-curatedtcgadata

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Homepage:

https://bioconductor.org/packages/3.17/data/experiment/html/curatedTCGAData.html

License:

Artistic-2.0

Recipe:

/bioconductor-curatedtcgadata/meta.yaml

This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.

package bioconductor-curatedtcgadata

versions:

1.22.2-0,  1.20.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0, 

1.22.2-0,  1.20.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-experimenthub:

>=2.8.0,<2.9.0

depends bioconductor-hdf5array:

>=1.28.0,<1.29.0

depends bioconductor-multiassayexperiment:

>=1.26.0,<1.27.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

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-curatedtcgadata

and update with::

   mamba update bioconductor-curatedtcgadata

To create a new environment, run:

mamba create --name myenvname bioconductor-curatedtcgadata

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-curatedtcgadata:<tag>

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

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