sc.get.aggregate summary statistics
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- Dominant language
- Python
- Stars
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- Avg merge
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- Merged PRs (30d)
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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
It would be nice if sc.get.aggregate provided a way to compute summary statistics and put them in .obs of the aggregated AnnData object.
Most important would be for me to store the number of cells per aggregated sample, for being able to filter out samples below a certain threshold.
Not even sure if there are other metrics that are relevant, but in the most general case it would take a callback function.
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 with the sc.get.aggregate entry point and the aggregated AnnData object's .obs behavior. Clarify which summary statistics are supported, how cell counts are represented, and whether callback results are accepted; the work is done when the interface and stored outputs are defined and implemented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100