Weighted directed graph analysis
sandra...@gmail.com
I tried to use Centiscape, but the app took almost the whole day to do calculations on a 12-node graph with around 23,000 edges. In spite of the long hours (this is my smallest graph), the app did not yield results (had to shut down while it was still calculating)
Grateful for any advice!
Sandeep Amberkar
Sandeep Amberkar
--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.
To post to this group, send email to cytoscape-helpdesk@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/91860ca9-2a59-4380-97f4-77df53ee2e21%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Sandra Alday
Great, thanks very much for pointing me to igraph. I’ll check that one out.
Many thanks,
Sandra
From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com]
On Behalf Of Sandeep Amberkar
Sent: Friday, 1 September 2017 7:43 PM
To: cytoscape...@googlegroups.com
Subject: Re: [cytoscape-helpdesk] Weighted directed graph analysis
What kind of analysis are you looking for?
Do you want to perform network centrality analysis? For that, you may be better off using the 'igraph' package (http://igraph.org/) which is written in Python and R, which makes these intense computations easier.
If your data consists of biological signaling networks, Cytoscape would best serve to visualise, you can't hope to perform any numerical computations within it. For these purposes, MATLAB and its ample toolboxes would serve your purpose.
Hope that helps.
Best,
Sandeep
--
Warm Regards,
Sandeep Amberkar
On 1 September 2017 at 01:07, <sandra...@gmail.com> wrote:
Which app is best to do an analysis of a weighted directed graph? I have several complex networks of between 12 - 25 nodes and thousands of edges.
I tried to use Centiscape, but the app took almost the whole day to do calculations on a 12-node graph with around 23,000 edges. In spite of the long hours (this is my smallest graph), the app did not yield results (had to shut down while it was still calculating)
Grateful for any advice!
--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/91860ca9-2a59-4380-97f4-77df53ee2e21%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
cytoscape-helpd...@googlegroups.com.
To post to this group, send email to
cytoscape...@googlegroups.com.
Visit this group at
https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CAKOge2Vu5-oGX%2BH3kb4-A1XR0rvSryqiGPEXS88NpTuZaNNi6A%40mail.gmail.com.
