Node deletion & parameter estimation

[Pranavathiyani G]

Hi,

I have a large network of about thousands of nodes, and I wish to calculate the network topological parameters i.e, degree, cc, shortest path, etc (which I did for the whole network).

But I would like to calculate the robustness or change in network topology by deleting nodes (one or two at the same time).

How can I perform such using cytoscape automation? Any help would be highly appreciated.

Thank you.

Pranavathiyani G

[Alexander Pico]

Network analyzer is one of the few functions we have not yet automated. We are working on a new version now which will support commands and will then be added to RCy3. We should have beta version out and ready for testing in the next month. 

For now, I’d recommend using RCy3 together with igraph to perform this set of operations. There is a vignette in the RCy3 package on how to do this. 

 - Alex

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[Giovanni Scardoni]

Hi,

This kind of analysis can be automatically done using the interference app. Unfortunately is not yet available for cytoscape 3.0, but you can download cytoscape 2.x and the interference app and it works.

See here:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088938

And download the app here:

http://www.cbmc.it/~scardonig/interference/InterferenceDownload.php

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