Yusuf Roohani

Thanks for your question and sorry for the late reply. Can you please share the output to adata.obs.head(). There might be an issue with the formatting What do you mean...

Thanks for your question. @cbirchsy This notebook contains all the information needed for preprocessing a scanpy AnnData object in general and this is what we use for any new dataset....

@monoplasty What do you mean by perturbation set

Thanks for your question. The condition column just refers to the gene that is perturbed within each cell. It is usually provided in the `.obs` metadata within the `AnnData` object....

Sorry for the very late response here. I will upload the data preprocessing script soon. In the meantime, you can directly load the replogle dataset using the appropriate arguments https://github.com/snap-stanford/GEARS/blob/df09d7ae34e90f5ef25afa389daf7c5c589e710d/gears/pertdata.py#L150-L152

Hi thanks for pointing this out. Yes, you are right that this is an error. Will fix in the next version after running some tests. For now, it should only...

Sorry for the delayed response! It's hard to follow exactly which dataset you used for training but if I understand correctly you tried using non-perturb seq data to train GEARS....

Closing due to lack of activity