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openvax / vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy
Apache License 2.0
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A way from VCF format to mutated peptides only #187

Closed nishuai closed 4 years ago

nishuai commented 4 years ago

Hi Alex,

Thank you for developing Vaxrank, your pipeline is the earliest and most easy-to-use pipeline for antigenic peptide prediction I have seen so far!

I wonder is there a way for me to use only part of your code to generate mutated peptides of some certain length, we would like to have peptide sequences to have a look at the general properties surrounding the mutated sites.

Thank you for your help.

Best

armish commented 4 years ago

Hi @nishuai,

If I am understanding your question right, varcode, which vaxrank depends on, should give you that functionality. The README and this probably a bit out-dated notebook should help you get started.

Hope this helps.

nishuai commented 4 years ago

Hi @armish ,

That's great, it seems to be exactly what I am looking for, thank you very much 👍