Bipartite network analysis using cytoscape

Question

[The Last Word]

Hi,

I have a bipartite network of transcription factors and genes. I used network analyzer in Cytoscape and got a very low density for the network which is to be expected if density measurement is done for the network in the conventional way. I however found a paper which disputed that all measurements for bipartite networks should be done differently due to its very nature (reference). I have two questions

1) Does Cytoscape have an app that specifically works to get measurements from bipartite networks?

2) If not, I would like to explain in my paper that the density of the network is low and its diameter is large due to its bipartite nature. Are there any publications you are aware of that I could use to reference such a statement.

[xanderpico]

You might try the Centiscape app. I'm not sure if it handles bipartite graphs, but it is a popular alternative to the built-in Network Analyzer.

http://apps.cytoscape.org/apps/centiscape

Answer 1

[xanderpico]

You might try the Centiscape app. I'm not sure if it handles bipartite graphs, but it is a popular alternative to the built-in Network Analyzer.

http://apps.cytoscape.org/apps/centiscape