Possible enhancement: multithreaded (via numba) mann-whitney tests
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- Dominant language
- Python
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Description
- Additional function parameters / changed functionality / changed defaults?
I recently wrote up a parallelized implementation of the Mann-Whitney U test, for my own use (gist is here). For the types of tests we tend to do in scRNAseq (lots of different features, 2d arrays) it basically scales with the number of cores you can throw at it. When you're doing a lot of tests this is very nice!
Given that scanpy already has a dependency on numba this would be a pretty simple thing to add, if you want to do so. Thought I would just point it out!
- James
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 linked gist and locating Scanpy's existing Mann-Whitney test entry point. Compare the proposed parallelized behavior with the current implementation, then define the supported API and validation needed before considering the enhancement complete.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, performance
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100