Introduce GLM-PCA to scanpy.external
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
I agree with @adrianveres here: GLM-PCA by @willtownes seems like a rigorous way to deal with zero inflation, since we use PCA as base for all subsequent processing. It’s apparently much faster than e.g. ZINB-WaVE
- twitter thread explaining the problem and solution
- code
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
Review the linked scrna2019 code and the scanpy.external entry point to understand the requested GLM-PCA integration. Confirm the intended scope and acceptance criteria with maintainers; done means GLM-PCA is available through scanpy.external with validation that matches the project’s expectations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100