Request: add PR-AUC metric
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- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
Similar to my request at the Seurat package, it would just be really nice if the precision-recall area under curve (PR-AUC) could be added alongside the AUC metric in the "top_genes.py" and "top_genes_visual.py" files.
PR-AUC is especially handy when dealing with imbalanced datasets (e.g. most sub-populations in a scRNA-seq experiment).
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 reading the existing AUC handling in scanpy/tools/top_genes.py and scanpy/plotting/top_genes_visual.py, including how the two entry points expose and display metrics. Done means PR-AUC is available alongside AUC in both files, with behavior appropriate for imbalanced single-cell populations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100