Can anyone tell me what diffusion algorithm is used by the tool diffusion in Cytoscape? Also, I found a plugin genemania in Cytoscape, does it do the same thing? I wish to get heat scores for the proteins in my network by providing a subset of proteins from this network as the positive set to genemania.
Thank you
The diffusion algorithm is described in the paper: Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017 Oct;13(10):e1005598. doi: 10.1371/journal.pcbi.1005598. eCollection 2017 Oct. PubMed PMID: 29023449; PubMed Central PMCID: PMC5638226. GeneMANIA uses a different algorithm completely which you can read about here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447538/