recipe bioconductor-curatedtcgadata

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

Homepage:

https://bioconductor.org/packages/3.16/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:

1.20.0-0,  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, 

1.20.0-0,  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 >=3.6.0,<3.7.0

• bioconductor-data-packages >=20221106

• bioconductor-experimenthub >=2.6.0,<2.7.0

• bioconductor-hdf5array >=1.26.0,<1.27.0

• bioconductor-multiassayexperiment >=1.24.0,<1.25.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• curl

• r-base >=4.2,<4.3.0a0

Required By:

• bioconductor-amaretto

• bioconductor-bioconcotk

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-curatedtcgadata

and update with:

conda update bioconductor-curatedtcgadata

or 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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