Package Recipe 'bioconductor-pgxrpi'

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:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-attempt
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-dplyr
on r-future
on r-future.apply
on r-ggplot2
on r-httr
on r-lubridate
on r-survival
on r-survminer
on r-yaml

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-pgxrpi

to add into an existing workspace instead, run:

pixi add bioconductor-pgxrpi

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-pgxrpi

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pgxrpi

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-pgxrpi/README.html)