recipe bioconductor-tcgautils

TCGA utility functions for data management

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/TCGAutils.html

License:

Artistic-2.0

Recipe:

/bioconductor-tcgautils/meta.yaml

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

package bioconductor-tcgautils

Versions:

1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.1-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicdatacommons >=1.22.0,<1.23.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-multiassayexperiment >=1.24.0,<1.25.0

• bioconductor-raggedexperiment >=1.22.0,<1.23.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-rvest

• r-stringr

• r-xml2

Required By:

• bioconductor-cbioportaldata

• bioconductor-terratcgadata

• bioconductor-rtcgatoolbox

Installation

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

conda install bioconductor-tcgautils

and update with:

conda update bioconductor-tcgautils

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-tcgautils:<tag>

(see bioconductor-tcgautils/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tcgautils/README.html)