how to do sub-module discovery from a reference network automatically

[Tongjun Gu]

Hello, I got differential expressed (DE) genes from many comparisons and would like to find the enriched sub-modules from the public available networks using jactivemodules. Since there are too many groups of DE genes to run, I can't do it by hand. Is there an approach to do it in batch using linux command line without graphic interface? I found there is command line in the newest version of cytoscape, but can't find the manual how to use it. How can I input the DE genes with fold change and P value, and save the lists of genes from each submodule into different files? Thank you very much!

[Christian Lopes]

Hi,

Can you please submit your question to the cytoscape-helpdesk group instead?

This one is used for the old Cytoscape Web project (Flash version):

Please use this one for Cytoscape (desktop application) questions:

https://groups.google.com/forum/#!forum/cytoscape-helpdesk

Thanks,

Christian

On Mon, Jan 16, 2017 at 5:42 PM, Tongjun Gu <tong...@gmail.com> wrote:

Hello, I got differential expressed (DE) genes from many comparisons and would like to find the enriched sub-modules from the public available networks using jactivemodules. Since there are too many groups of DE genes to run, I can't do it by hand. Is there an approach to do it in batch using linux command line without graphic interface? I found there is command line in the newest version of cytoscape, but can't find the manual how to use it. How can I input the DE genes with fold change and P value, and save the lists of genes from each submodule into different files? Thank you very much!

--
You received this message because you are subscribed to the Google Groups "cytoscapeweb-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscapeweb-discuss+unsub...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.