outlier detection in scanpy?
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
Hi there,
instead of a fixed mito-percent cutoff that I have to set each time, does scanpy have some automated way of finding outliers of some heuristic to find a reasonable cutoff?
If not, do you think 5% is a good cutoff for most datasets?
I'm looking for a scanpy function similar to detect_outliers() in the R package scPipe.
Sorry if this has been asked before, I did some searching in the issues but couldn't find anything.
best
Max
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 Scanpy's existing quality-control and mitochondrial-percentage filtering entry points, then compare their behavior with scPipe's detect_outliers(). Determine whether the requested automated heuristic is already available; done would require a clearly scoped decision about adding or documenting such functionality, including how a reasonable cutoff is established.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100