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theislab / scgen

Single cell perturbation prediction
https://scgen.readthedocs.io
GNU General Public License v3.0
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Batch effect removal with only one cell type #60

Closed ryeking2010 closed 2 years ago

ryeking2010 commented 2 years ago

Hello,

Is it possible to remove batch effects when giving all the cells the same label?

Will this prevent the loss function from properly optimizing the parameter values in the neural network?

We have isolated the same cell type from many batches and hope to remove the batch effect to study subtypes.

Thank you in advance for your assistance!

M0hammadL commented 2 years ago

Hi Sorry for late reply,

I think it would not be ideal if you don't know the subtype labels, I would suggest checking out scArches : https://github.com/theislab/scarches