How to access Cytoscape apps within R

Question

[Muny]

Im wondering if there is a way to access Cytoscape installed apps from R Studio. I have recently installed the GeneMANIA app in Cytoscape and would like to query lists of genes without having to use the Cytoscape app as this part of the process will be automated. I am having trouble finding documentation for the commands and was wondering if anyone knew of available resources. Thank you in advance.

Answer 1

[scooter]

The short answer is absolutely! Take a look at RCy3 -- it is an R package that provides access to Cytoscape, including any Cytoscape app that supports automation (which GeneMANIA does). RCy3 is available via BioConductor and is actively being developed in conjunction with Cytoscape itself. (For python developers, you may want to look at py4cytoscape, which, like RCy3 is under active development).

-- scooter

[Muny]

Thank you very much!