Cytoscape Diffusion Algorithm

Question

[Nazifa Ahmed]

Hi,

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

[Ram]

Stick to one question instead of asking multiple questions in the same thread.

Answer 1

[xanderpico]

GeneMANIA does not perform diffusion. The diffusion tool calls a web service. Here is the code for the web service: https://github.com/idekerlab/heat-diffusion/blob/master/heat_diffusion_service.py