sc.pp.filter_cells does not work for pseudo counts data
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
Hi all, I have some pseudo counts data, which containing value like 0.5, and if I run sc.pp.filter_cells based on this dataset, the filtered number of cells is very low. I wonder if the codes of sc.pp.filter_cells are updated or not, and how to handle such pseudo counts scRNA-seq data based on scanpy. Thanks a lot.
The dataset I used is https://portal.hubmapconsortium.org/browse/dataset/fd57a928d9f3cee7e95d284f1d5b9935
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 reproducing the reported result with the linked HuBMAP dataset and sc.pp.filter_cells, then inspect how the entry point handles fractional pseudo-count values. Done means the expected filtering behavior for pseudo-count scRNA-seq data is established and the issue is either resolved or documented with a verified result.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100