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openvax / vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy
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Include MHC expression in final report #41

Open iskandr opened 8 years ago

iskandr commented 8 years ago

The expression of individual alleles can be extracted from the output of seq2hla or alternatively we can try to recompute it ourselves (since we have the tumor RNA).

hammer commented 8 years ago

More generally expression of APM pathway genes would be nice to have

This issue should live in epidisco though not vaxrank?

iskandr commented 8 years ago

I guess it's an issue for both? Vaxrank needs to show the info and optionally include it in ranking criteria (downweight alleles which show little expression). Epidisco should probably coordinate computing expression (we can use standard quantification for TAP1/TAP2/ERAP1/ERAP2/TAPBP but need something special for MHCs).

iskandr commented 8 years ago

Forgot about this, @ihodes @julia326 we'll probably look at this manually for the first patient but we might want to think about parsing seq2hla's expression file format.