Package Recipe 'bioconductor-cbpmanager'

recipe bioconductor-cbpmanager

Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/cbpManager.html
License:: AGPL-3 + file LICENSE
Recipe:: /bioconductor-cbpmanager/meta.yaml

This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.

package bioconductor-cbpmanager¶

Versions:

1.18.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-basilisk >=1.22.0,<1.23.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-dt
on r-htmltools
on r-jsonlite
on r-magrittr
on r-markdown
on r-plyr
on r-rapportools
on r-reticulate
on r-rintrojs
on r-rlang
on r-shiny
on r-shinybs
on r-shinycssloaders
on r-shinydashboard
on r-vroom

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-cbpmanager

to add into an existing workspace instead, run:

pixi add bioconductor-cbpmanager

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-cbpmanager

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cbpmanager

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-cbpmanager:<tag>

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