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theislab / scarches

Reference mapping for single-cell genomics
https://docs.scarches.org/en/latest/
BSD 3-Clause "New" or "Revised" License
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Can trVAE in scarches be applied to perturbation prediction? #239

Closed weizhiting closed 2 months ago

weizhiting commented 4 months ago

Hi, In the original trVAE, trVAE can be used to perturbation prediction. I wonder whether trVAE in scarches can be applied to perturbation prediction? In scarches demo case, trVAE was used to remove batch effect.

M0hammadL commented 4 months ago

hi @chelseabright96 , could you please add a tutorial similar to this one https://github.com/theislab/trVAE/blob/master/examples/trVAE_Haber.ipynb using the Python version of trvae as in here https://github.com/theislab/scarches/blob/master/notebooks/trvae_surgery_pipeline.ipynb

weizhiting commented 2 months ago

Thanks for your reply.