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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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Incorporate predictions from TCRMatch #755

Open malachig opened 2 years ago

malachig commented 2 years ago

This would be one way to integrate consideration of TCR repertoire data. If a user has TCR data from TILs say, they could use TCRMatch to further prioritize candidates where TCRMatch reports a hit in IEDB or CEDAR (similar TCR) and the known epitope for that match is similar to the candidate neoantigen peptide from pVACtools.

malachig commented 2 years ago

Or, if the user does not have TCRseq data, candidate TCRs could be mined from bulk RNA-seq data from the tumor, using a tool such as TRUST4.