recipe bioconductor-tcgautils

TCGA utility functions for data management

Homepage:

https://bioconductor.org/packages/3.18/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:

1.22.0-0,  1.20.2-0,  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, 

1.22.0-0,  1.20.2-0,  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:

>=1.64.0,<1.65.0

depends bioconductor-biocbaseutils:

>=1.4.0,<1.5.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicdatacommons:

>=1.26.0,<1.27.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

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-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-rvest:

depends r-stringr:

depends r-xml2:

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-tcgautils

and update with::

   mamba update bioconductor-tcgautils

To create a new environment, run:

mamba create --name myenvname bioconductor-tcgautils

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-tcgautils:<tag>

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

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