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/3.17/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:

1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-basilisk:

>=1.12.0,<1.13.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-dt:

depends r-htmltools:

depends r-jsonlite:

depends r-magrittr:

depends r-markdown:

depends r-plyr:

depends r-rapportools:

depends r-reticulate:

depends r-rintrojs:

depends r-shiny:

depends r-shinybs:

depends r-shinycssloaders:

depends r-shinydashboard:

depends r-vroom:

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-cbpmanager

and update with::

   mamba update bioconductor-cbpmanager

To create a new environment, run:

mamba create --name myenvname bioconductor-cbpmanager

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-cbpmanager:<tag>

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

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