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theislab / scCODA

A Bayesian model for compositional single-cell data analysis
BSD 3-Clause "New" or "Revised" License
141 stars 23 forks source link

Tutorial for R/reticulate #83

Closed ConDem94 closed 4 months ago

ConDem94 commented 11 months ago

Is it possible to perform scCODA analysis in R using reticulate?

Thank you, Constantinos

johannesostner commented 11 months ago

Hi! We haven't tried using scCODA with reticulate, but I think this should be possible. As always when using cross-language links, you should make sure that all dependencies are installed and the richt python instance is loaded through reticulate. I'm also not sure whether using the wrappers around ALDEx2/ANCOM in the package is possible, as they are executed in R through rpy2. Our latest implementation of scCODA in pertpy does not have these R dependencies, if they should cause any issues with reticulate

adityamahadevaniyer commented 8 months ago

Sccoda doesn’t work in reticulate using pertpy. Please check this issue https://github.com/theislab/pertpy/issues/402

Zethson commented 8 months ago

@adityamahadevaniyer we're already discussing it over there. Patience please :)