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LouisFaure / scFates

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
https://scfates.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
50 stars 2 forks source link

citing CellRank #2

Closed Marius1311 closed 3 years ago

Marius1311 commented 3 years ago

Hi scFates Team, thanks for this great tool! Looks fantastic, eager to check it out. Also, I'm excited that you use CellRank, seems like there are some synergies there. Just one thing, could you please add CellRank to your references and add a link/citation to your tutorial? Thanks!

LouisFaure commented 3 years ago

Dear @Marius1311,

Thank you for your interest in scFates! Your tool CellRank is indeed quite powerful to obtain lineages, so I thought it could be combined with scFates for more robust bifurcation analysis!

I just updated the documentation and the notebook with the reference to your preprint, the notebook was in need anyway of an introduction of CellRank, with an explanation of the rationale behind the conversion.

I also re-used your implementation of the Fisher test for the correlations from your function lineages_drivers on the newly introduced tl.criticality_drivers (as you can see I even borrowed part of the name ;) ).

I now clearly mention the part re-used in the code as well as in the API documentation!

Please let me know if this suits you!

Marius1311 commented 3 years ago

Amazing, @LouisFaure, thank you very much! That's perfect.