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theislab / scgen

Single cell perturbation prediction
https://scgen.readthedocs.io
GNU General Public License v3.0
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Can I use scGen for Drug Responder and Non-responder prediction? #27

Closed levinhein closed 3 years ago

levinhein commented 4 years ago

Hello. I have a Seurat object where all cells are each labeled as "R" for responder and "NR" for non-responder under the Seurat object metadata column "response". I wonder if I can use scGen to predict a patient's scRNAseq data as: R or NR. I only have responder and non-responder labels on the cells after drug treatment, not a "before and after" scRNAseq. scGen can predict the single-cell gene expression, but can I use it to identify people as drug responder and non-responder? Any insights on how the implementation will be?

M0hammadL commented 4 years ago

Hi Levine, scGen can predict the gene expression after the perturbation, the problem that you are referring to is a a binary classification that says yes (R) or no (NR). scGen does that in essence by predicting the response with a small value but still, it is expression profile, not a yes or no question. I would suggest training a simple classifier to predict that for u.