STARsolo Matrix with Velocyto --> Anndata function
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- Dominant language
- Python
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Description
The scanpy.read_10X_mtx works well for reading in the STARsolo output matrices, which are based on the CellRanger Outputs.
However, it would be nice to have a function or modification of the read_10X_mtx function (e.g. a boolean for STARsolo velocyto) to automate inputting the velocyto matrices that STARsolo outputs and placing them in the appropriate layers. A boolean switch for filtered versus raw matrices would be a good addition 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 by reading scanpy.read_10X_mtx and the STARsolo output matrix conventions described in the issue. Define the supported Velocyto inputs and filtered-versus-raw behavior, then verify that the resulting matrices are placed in the appropriate layers; the issue does not name tests or files to run.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100