search

PadiLab / CRANE

GNU General Public License v3.0
2 stars 0 forks source link

Question about CRANE #3

Open aldosc opened 1 month ago

aldosc commented 1 month ago

Hi,

I interested in running CRANE for a network analysis. I been trying the implementation in the NetZooR package. In the paper it's mentioned that CRANE can be used with other methods outside of the NetZoo ecosystem. For example, this could be the case for different module detection algorithms. Do you have an example of what could be the inputs for CRANE outside of NetZoo?

Thanks

meghapadi commented 2 weeks ago

Hi, Thank you for your question, and sorry for the delay - I was away from the office. There are two ways you could use CRANE.

1) Input a set of differential modules. This is how CRANE is designed for use (as the next step after running ALPACA). CRANE will then compute p-values for each node. You can use ALPACA to identify the differential modules, or you could use a different method. For example, you could compute the delta edge weights between the two networks and run Louvain, or your favorite community detection method from igraph.

2) Input a weighted bipartite graph. A function within CRANE can be used to generate a null distribution for the weighted bipartite graph. Then you could measure any feature of your disease network (e.g. clustering coefficient, betweenness, CONDOR module connectivity) and compute an empirical p-value. This option is not automatically available as part of the CRANE package but could be custom-coded by the user.

I hope this helps. Let me know if you have further questions.

Best, Megha

Megha Padi, Ph.D. Assistant Professor, Molecular and Cellular Biology Applied Mathematics - GIDP Cancer Biology - GIDP University of Arizona Website: https://www.padilab.com

On Tue, Aug 6, 2024 at 9:39 AM aldosc @.***> wrote:

Hi,

I interested in running CRANE for a network analysis. I been trying the implementation in the NetZooR package. In the paper it's mentioned that CRANE can be used with other methods outside of the NetZoo ecosystem. For example, this could be the case for different module detection algorithms. Do you have an example of what could be the inputs for CRANE outside of NetZoo?

Thanks

— Reply to this email directly, view it on GitHub https://github.com/PadiLab/CRANE/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5P46LXOJ62YKB7O37S4GTZQD33VAVCNFSM6AAAAABMCWTRQSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ2TCMRZGM2DCMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>