recipe bioconductor-pgxrpi

R wrapper for Progenetix

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/pgxRpi.html

License:

Artistic-2.0

Recipe:

/bioconductor-pgxrpi/meta.yaml

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

package bioconductor-pgxrpi

versions:

1.2.0-0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-attempt:

depends r-base:

>=4.4,<4.5.0a0

depends r-circlize:

depends r-dplyr:

depends r-future:

depends r-future.apply:

depends r-ggplot2:

depends r-httr:

depends r-lubridate:

depends r-survival:

depends r-survminer:

depends r-yaml:

requirements:

additional platforms:

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-pgxrpi

and update with::

   mamba update bioconductor-pgxrpi

To create a new environment, run:

mamba create --name myenvname bioconductor-pgxrpi

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-pgxrpi:<tag>

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

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Link to this page

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