proposal for friendly spatialdata_io.stereoseq function
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- python
- Domain
- bioinformatics, data
Research direction
Start by inspecting the spatialdata_io.stereoseq reader and comparing the files produced by SAW's count command with the files expected by the reader, especially the missing cell.cluster file. Review the alternate SAW analysis output and the proposed Visium-style directory and GEF/GEM inputs. Done requires a decided compatibility scope and a documented, working reading path.
Written by the indexing model from the issue text.
Description
Encountering an issue with missing files when reading BGI's stereo seq data, and there is an inconsistency between the output files from the count command of SAW (a tool under BGI's technology similar to 10x spaceranger) and what is read by spatialdata_io.stereoseq.
Specifically want to know if it is because the SAW output has been updated, making it incompatible with the file reading command of spatialdata_io (there is no cell.cluster file, but it exists in another analysis command of SAW output file).
My proposal is whether there can be a simple reading script (such as one that can just read the 10x Visium output directory and create zarr data) for easy reading(gef gem file).
- Dominant language
- Python
- Stars
- 103
- Forks
- 64
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Getting set up
- No Dockerfile or Docker Compose file
- No pull request template
- Read the contributing 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.
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