Add non-negative matrix factorization for cell-by-peak matrix?
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- Dominant language
- Python
- Stars
- 323
- Forks
- 43
- PR merge metrics
- No merged PRs in 30d
Description
Hi Kai,
I used Yang Li's previous non-negative matrix factorization (nmf) pipeline (with some modifications by myself) to analyze the modules for pseudo-bulk level cell-by-peak matrix.
https://github.com/beyondpie/CEMBA_wmb_snATAC/tree/main/04.nmf
Do you think we can wrap us this into a module for SnapATAC2?
Songpeng
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Research direction
Start by reviewing the linked 04.nmf pipeline and comparing its behavior with SnapATAC2's existing analysis modules. Determine the intended API, inputs, outputs, and tests for wrapping non-negative matrix factorization of a pseudo-bulk cell-by-peak matrix; the issue is complete when this scope and validation are defined and implemented.
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Assessment
- Tech stack
- python
- Domain
- data, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100