Estimation of relatedness in parasites from a single infection using single cell RNA seq data
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 20/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
No source file, test, or entry point is identified. Start by reviewing dcifer's existing relatedness approach and the cited single-cell DNA IBD work, then determine whether sparse single-cell RNA genotypes can be supported. Done would require an agreed method and validation showing reliable relatedness estimates for single infections.
Written by the indexing model from the issue text.
Description
Dear developer,
Many thanks for the great tool! It will be very impactful for the community as shown by its application to the Zanzibar dataset.
Is it possible to adapt the tool to estimate relatedness between strains within 1 infection? IBD has been demonstrated for this using single-cell DNA data in this paper ( https://doi.org/10.1016/j.chom.2019.12.001 ) but i'm struggling to implement it for much more sparse genotypes from single-cell RNA data and I was wondering whether your tool can be used for this.
I will be grateful for any feedback. Thanks!
- Dominant language
- C
- Stars
- 8
- Forks
- 5
- PR merge metrics
- No merged PRs in 30d
Getting set up
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First steps
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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