scverse / scverse/spatialdata-io
VisiumHD: Reading in raw_probe_bc_matrix.h5
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- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
spatialdata_io.visium_hd() now allows users to select between 'raw_feature_bc_matrix.h5' and 'filtered_feature_bc_matrix.h5', but in the output of Space Ranger, there is also the 'raw_probe_bc_matrix.h5' file, which allows the analysis of counts on a probe-level (instead of collapsing the counts of all probes into a single feature). While more niche, there are definitely situations where it would be very valuable if spatialdata_io.visium_hd() would support reading in this file (e.g. in cases of (partial) gene deletions) as well.
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 at spatialdata_io.visium_hd() and compare how it selects between raw_feature_bc_matrix.h5 and filtered_feature_bc_matrix.h5. Investigate the Space Ranger raw_probe_bc_matrix.h5 input and its probe-level counts. Done means visium_hd() can read this file while retaining probe-level counts for downstream analysis.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100