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openvax / vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy
Apache License 2.0
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Depend on topiary #31

Open hammer opened 8 years ago

hammer commented 8 years ago

Topiary and Vaxrank have different end users but it would be nice nice to reuse some of the minimal epitope ranking logic in topiary within the SLP ranking logic in Vaxrank.

iskandr commented 8 years ago

This would probably entail moving/merging the following files into Topiary:

https://github.com/hammerlab/vaxrank/blob/master/vaxrank/epitope_prediction.py https://github.com/hammerlab/vaxrank/blob/master/vaxrank/mutant_protein_fragment.py

As well as exposing isovar as a second method for determining protein sequences within Topiary.

tavinathanson commented 7 years ago

From @hammer:

we really need to prioritize the topiary/vaxrank integration [...] i’m concerned about results diverging across cohorts and epidisco due to that