griffithlab / griffithlab/pVACtools
Incorporate predictions from TCRMatch
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 188
- Forks
- 81
- Avg merge
- 9d 17h
- Merged PRs (30d)
- 6
Description
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.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue names no files, tests, or entry points. Start by identifying where pVACtools prioritizes candidate neoantigen peptides and what input and output data TCRMatch would require; done should include a defined integration that uses reported TCRMatch hits and epitope similarity to prioritize candidates.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100