scanpy.pp.filter_genes should have a batch key option
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
It would be great if scanpy.pp.filter_genes had a batch key option so that options like min_counts were taken with respect to each batch.
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 scanpy.pp.filter_genes entry point and trace how min_counts and related thresholds are currently applied. Determine the expected behavior when a batch key is provided, including how batches are identified and how filtering results are combined. Done means the option works consistently per batch and its behavior is covered by appropriate tests and documentation.
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
- 35/100