- recipe bioconductor-cbaf
Automated functions for comparing various omic data from cbioportal.org
This package contains functions that allow analysing and comparing omic data across various cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.
- package bioconductor-cbaf¶
- depends bioconductor-biocfilecache:
- depends bioconductor-cbioportaldata:
- depends bioconductor-genefilter:
- depends r-base:
- depends r-gplots:
- depends r-openxlsx:
- depends r-rcolorbrewer:
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-cbaf and update with:: mamba update bioconductor-cbaf
To create a new environment, run:
mamba create --name myenvname bioconductor-cbaf
myenvnamebeing 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-cbaf:<tag> (see `bioconductor-cbaf/tags`_ for valid values for ``<tag>``)