Best Clustering App?

[Daniel M.]

Hi, I'm pretty new to Cytoscape but it looks pretty awesome so far! 
Can I get some opinions on what the best clustering apps (plugins) are?  
I'm looking to cluster a social network.  

Here are some features I'd like to see in a clustering app:

--Clusters networks (duh)

--app that returns metrics about clusters (eg: average within cluster distance).  
--App that not only clusters networks but can use algorithms (such as the gap statistic) to know when to STOP clustering

Any ideas?  Thanks guys!

[alex.pico]

Hi Daniel,

The answer to the first part of your question is pretty easy:  clusterMaker 2 http://apps.cytoscape.org/apps/clustermaker2
This is a pretty comprehensive clustering solution, with over two dozen algorithms supported and developed primarily by a core Cytoscape developer with over a dozen Cytoscape apps to his name, Scooter Morris. And, I'll have to leave the more detailed aspects of your question to him...

Cheers,
 - Alex

[Scooter Morris]

Hi Daniel,
    I can answer some of your questions, but most are very algorithm-dependent.  In general, clusterMaker2 reports modularity as a metric, which is a measure of the number of internal edges vs. the number of external edges.  I've thought of adding silhouette as an alternative measure since I already have the code for other clustering algorithms (e.g. K-Means).  As far as when to stop clustering -- each of the algorithms has it's own measure for convergence, or is limited by a specific number of iterations.

-- scooter

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