griffithlab / griffithlab/pVACtools
Incorporate gene of interest status in the aggregate tiering/sorting
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 188
- Forks
- 81
- Avg merge
- 9d 17h
- Merged PRs (30d)
- 6
Description
https://github.com/griffithlab/pVACtools/pull/1229 incorporates a new feature where epitopes resulting from variants on a gene of interest are marked. This information could be used to further refine the aggregate report. Some options are:
- Give priority to predictions on a gene of interest when sorting the results among each tier
- Add a new tier for predictions that are are Pass and on a Gene of Interest and sort this tier above simple Pass predictions
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
Start by reviewing PR #1229 to understand how gene-of-interest status is represented, then trace the aggregate report's tiering and sorting behavior. Resolve whether the intended result is priority within existing tiers or a new tier above Pass, and verify the chosen behavior in aggregate report output.
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
- 30/100