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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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How are isofox neoepitiope files created? #270

Closed joe-usset closed 1 year ago

joe-usset commented 2 years ago

I am trying to find how the neoepitope files (*.isf.neoepitope.csv) from isofox are created. In particular, I want to understand the method used to predict neoepitope counts.

I have looked through ~/master/isofox/README.md but can't find a description. Where can I find more information?

Thank you for any help!

p-priestley commented 2 years ago

This is experimental functionality right now. We will likely release our full neoepitope toolset somewhere in the coming months

joe-usset commented 2 years ago

Ok, thank you.

alhafidzhamdan commented 2 years ago

Any updates re: neoepitope tools @p-priestley ?

p-priestley commented 2 years ago

Sorry. Still on the to do list, but have been focusing on other priorities. We hope later this quarter.

charlesshale commented 1 year ago

The neoepitope and peptide scoring pipeline is now described here: https://github.com/hartwigmedical/hmftools/tree/master/neo

and a demo pipeline shown here: https://github.com/hartwigmedical/hmftools/blob/master/pipeline/scripts/run_neo_pipeline