Gene network module identification methods

Question

[zhang.jianhai]

Dear community,

I am comparing gene network module identification methods. I have considered WGCNA, petal, Clust, GeneNet, Cross-Clustering, minet, and want as more as possible. What other methods do you recommend?

The methods I am interested in would have 1) R implementation 2) generate gene connection information, not just detect gene modules.

Regards