Package Recipe 'bioconductor-curatedpcadata'

recipe bioconductor-curatedpcadata

Curated Prostate Cancer Data

Homepage:: https://bioconductor.org/packages/3.22/data/experiment/html/curatedPCaData.html
License:: CC BY 4.0
Recipe:: /bioconductor-curatedpcadata/meta.yaml

The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in.

package bioconductor-curatedpcadata¶

Versions:

1.6.0-0

Depends:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-data-packages >=20260207
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-raggedexperiment >=1.34.0,<1.35.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on curl
on r-base >=4.5,<4.6.0a0
on r-reshape2
on r-rlang

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-curatedpcadata

to add into an existing workspace instead, run:

pixi add bioconductor-curatedpcadata

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-curatedpcadata

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-curatedpcadata

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-curatedpcadata:<tag>

(see bioconductor-curatedpcadata/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-curatedpcadata/README.html)