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Can trVAE in scarches be applied to perturbation prediction? #239

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weizhiting opened this issue Jun 2, 2024 · 1 comment · May be fixed by #243
Open

Can trVAE in scarches be applied to perturbation prediction? #239

weizhiting opened this issue Jun 2, 2024 · 1 comment · May be fixed by #243
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@M0hammadL @chelseabright96

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@weizhiting
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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
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M0hammadL commented Jun 4, 2024 •
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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

@chelseabright96 chelseabright96 linked a pull request Jun 6, 2024 that will close this issue
add trvae Perturbation prediction notebook #243
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add trvae Perturbation prediction notebook theislab/scarches
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@weizhiting @M0hammadL @chelseabright96