Pathway directory question

[ethanbahl]

Thank you for developing this tool, I have been looking for something like iPanda for a while now. I was able to successfully run the ipanda script on my own expression data with the sample_kegg data. Now I would like to analyze more pathways but I'm not sure how the files in the pathway directory were created. Most of those files seem straightforward to produce but I'm curious where I can find the topology coefficients for other KEGG pathways to put in a pathway_akk file.

Any advice would be greatly appreciated, and thanks again!

[varnivey]

Hi! Thank you for your interest in our tool.

Yes, the additional calculations should be performed to obtain the topology coefficients according to the procedure described in detail in the iPANDA paper:

https://www.nature.com/articles/ncomms13427

Please, contact me at ivan@insilicomedicine.com for the further information or in case any assistance is needed.

[immuneAI]

@ethanbahl @varnivey Can you help to add more pathways to the pathway directory.