Enhance scanpy.tl.rank_gene_groups with additional filters (min_pct, etc.,)
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Area – Differential Expression
- Dominant language
- Python
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Description
What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
The sc.tl.rank_gene_groups function needs additional arguments to filter some genes before running a test on them, just like Seurat's FindMarkers function.
minc_pct: Only test genes detected in a minimum fraction of min_pct cells in either of the two comparison groups. It is beneficial for comparing cluster A to cluster B.min_cells: Minimum number of cells expressing the feature in at least one of the two comparison groups.min_pct_difference: Only test genes showing a minimum difference in the detection fraction between the two comparison groups.
I will also try to implement these changes.
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 at the sc.tl.rank_gene_groups entry point and review how genes are selected before statistical testing. Compare the requested minc_pct, min_cells, and min_pct_difference behavior with Seurat's FindMarkers; done means the function supports these filters with behavior matching the stated comparison-group requirements.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100