diffxpy integration
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- Dominant language
- Python
- Stars
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- Avg merge
- 1d 4h
- Merged PRs (30d)
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
I'd really like a smarter d/e method to be accessible easily from Scanpy, one that allows proper treatment of covariates etc. MAST is obviously very popular, but fiddly to integrate from R. I see diffxpy mentioned about the place here, and see it's an in-house tool of yours. Is there a reason it's not been integrated already? If nobody's working on it, shall I take a crack at it?
Contributor guide
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 the existing sc.external and sc.tools entry points and how Scanpy exposes differential-expression methods. Then examine diffxpy's integration requirements, including covariate handling, and clarify the intended API and supported functionality. Done means a documented, tested Scanpy-accessible integration is agreed and implemented.
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