search

EPPIcenter / dcifer

Distance for Complex Infections: Fast Estimation of Relatedness (R package)
https://eppicenter.github.io/dcifer/
Other
5 stars 4 forks source link

Estimation of relatedness in parasites from a single infection using single cell RNA seq data #1

Open JesseRop opened 1 year ago

JesseRop commented 1 year ago

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!

innager commented 1 year ago

Thank you, this is an interesting question. In its current version, you can similarly use Dcifer for pairwise comparisons of strains as if they were monoclonal infections. Going forward, we might look at developing a version specifically for single-cell data.