BioPlex R/Python Packages
About BioPlex R/Python Packages
CCB implemented programmatic access to the BioPlex PPI networks and integration with related resources from within R and Python. Besides PPI networks for 293T and HCT116 cells, this includes access to CORUM protein complex data, PFAM protein domain data, PDB protein structures, and transcriptome and proteome data for the two cell lines. The implemented functionality serves as a basis for integrative downstream analysis of BioPlex PPI data with domain-specific R and Python packages, including efficient execution of maximum scoring subnetwork analysis, protein domain-domain association analysis, mapping of PPIs onto 3D protein structures, and analysis of BioPlex PPIs at the interface of transcriptomic and proteomic data.
Objectives: (1) implement programmatic access to BioPlex from within R/Bioconductor, (2) implement programmatic access to BioPlex from within Python, and (3) implement a series of downstream applications of BioPlex, thereby connecting the data to domain-specific R and Python analysis and visualization packages.
Publications
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BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions
Authors: Ludwig Geistlinger, Roger Vargas, Jr, Tyrone Lee, Joshua Pan, Edward L Huttlin, Robert Gentleman
Bioinformatics, Volume 39, Issue 3, March 2023