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wukevin / babel

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
https://www.pnas.org/content/118/15/e2023070118
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CITEseq / protein applications #14

Open fisherj-2212 opened 7 months ago

fisherj-2212 commented 7 months ago

Hi,

I am interested in the application of BABEL to multimodal RNA / protein data. You mention you have a proof of concept for this. Would you please be able to point me to the relevant file, and give some guidance on how to apply BABEL to CITEseq ?

fisherj-2212 commented 7 months ago

Updating to add that I've noticed separate functions for protein data called 'train_protein_predictor.py' and 'predict_protein.py'. Could you provide some guidance on what format the required arguments should take? What a typical function call might look like?

zhangxueting233 commented 4 weeks ago

I am also very interested,do you solve this problem？

fisherj2 commented 4 weeks ago

I ended up adapting the python functions provided in the scLinear repo , where the authors present a comparison of scLinear to BABEL. In particular, the method ADTPredictorBabel(), which is defined in a commented out section of prediction.py

zhangxueting233 commented 4 weeks ago

Thanks for your reply