navinlabcode / navinlabcode/CellTrek
Using Celltrek on non-matching data ST and SC data.
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- Dominant language
- R
- Stars
- 135
- Forks
- 23
- PR merge metrics
- No merged PRs in 30d
Description
Hello Celltrek devs,
I would like to map cells from a single-cell dataset which only includes one cell type to a spatial transcriptomics dataset which includes multiple cell types. Is this possible, and if so, is there anything I should keep in mind while doing so?
If this is not possible, are there any work-arounds, such as merging the single cell dataset with a reference dataset which includes additional cell types I would expect?
sincerely,
Dillon
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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
No file, test, or entry point is identified. Review the CellTrek mapping workflow and existing usage documentation, then determine whether a single-cell dataset containing one cell type can be mapped to a multi-type spatial transcriptomics dataset and document any supported workaround.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100