- recipe bioconductor-bioplex
R-side access to BioPlex protein-protein interaction data
The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.
- package bioconductor-bioplex¶
- depends bioconductor-biocfilecache:
- depends bioconductor-data-packages:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-geoquery:
- depends bioconductor-graph:
- depends bioconductor-summarizedexperiment:
- depends curl:
- depends r-base:
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-bioplex and update with:: mamba update bioconductor-bioplex
To create a new environment, run:
mamba create --name myenvname bioconductor-bioplex
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-bioplex:<tag> (see `bioconductor-bioplex/tags`_ for valid values for ``<tag>``)