Hi all,
I have cool metabolomic data that I am analyzing (this is in treatment naive, early stage MS). I was wondering if/how I might leverage Cytoscape for visualization? Any starter tips would be welcomed.
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@peixott @paularp @vdardov @ecebayram @ekaamewu @vcatterson @MYSchmidt @kathrynstep @mdeleeuw @SLeslie @mariariverapaz @marekpiatek wondering if this is a tool any of you have come across?
I never worked with it since I don’t due metabolomics unfortunately. But I saw some Parkinson’s papers that used this tool when I searched on google & pubmed. At times, the authors may share their codes, workflow on github etc. wonder if any of those papers included that 
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Hello all,
I have not used this tool before but I just looked it up and looks like something that will be great and fun to work with. I am going to explore it further, and I am sure you have seen this resource: Home · cytoscape/cytoscape-tutorials Wiki · GitHub
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For network visualization Cytoscape is huge. I played with Cytoscape during my Bachelor in computer science and it provides awesome plots. Another one that I remember to use is Pajek.
Now for analysis I really like to use the library NetworkX on Python and most of my networks I plot using yED (they accept the GML format, so it is really simple to export the GML and open and format on yED)
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I second the support for NetworkX in Python! It’s what I tend to use for network visualizations, too. However, it doesn’t always give you the best control over layout for very large networks. Cytoscape looks like it can handle large networks with very pretty visualizations! I’m afraid I don’t have any experience of using it, but I’ll test it out next time I’m working with a network diagram. Thanks for the heads-up!
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Thanks, y’all. I’ll definintely be exploring in the coming weeks (bandwidth permitting 
)
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