scverse / scverse/spatialdata-io
Visium in matrix market format
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- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
Probably tangentially related to #287 , however this is also a semi common issue for visium data. For example, the entire WUSTL pancreatic cancer cohort from the human tumor atlas cohort provides their data in the matrix market format. It seems similar to the format where there is a barcodes.tsv.gz, matrix.mtx, and features.tsv.gz in some older 10x single cell datasets. Would it be worth adding a function to recognize this format and read it?
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 related issue #287 and the repository's existing readers for Visium or 10x-style inputs. Compare how barcodes.tsv.gz, matrix.mtx, and features.tsv.gz are handled, then define completion as recognizing and successfully reading the described matrix market format with appropriate coverage.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100