How to install and run GenKI/notebook/SERGIO.py's environment? The use of scTenifoldpy (pip install scTenifoldpy) does not seem to match ogenki's environment.

Hi, @yjgeno @guanxunli @jamesjcai.
Thanks for the wonderful package.

I installed dependencies and GenKI following your instruction.
But I couldn't use your package because of an issue.
When I run the code below, jupyter notebook restart automatically with the message "the kernel appears to have died. it will restart automatically".

from GenKI.preprocesing import build_adata
from GenKI.dataLoader import DataLoader
from GenKI.train import VGAE_trainer

Could you help me solve this problem?

Thank you.

Hi!
Thanks for your perfect work! I'm looking for a method which can generate virtual perturbed data. When I notice GenKi can predict the effect after perturbation of certain target, I wonder if Genki could just generate the simulated KO data for independent analysis in addition to the initial goal. Besides, I am also concerned about if GenKI can perturb multiple genes simultaneously as a optional setting.
With best wishes!
cdd

Hi @yjgeno @jamesjcai @guanxunli

Thanks for developing GenKI. I was excited to use it to knockout a gene from Malaria Cell Atlas and see if it gives better results in terms of biology than scTenifoldKnk. Since the MCA atlas is large, nearly 29K cells, I split them into their sell stages and then tried running GenKI. I have 7K cells in current run and I am using 12 cores but it's been entire day and it seems to have stuck at DataLoader step.

Do you have any benchmark as to how much time will it take against number of cells?

Hi,

Thank you for providing the code.
Do you have the Rdata listed in the notebook?
data/microglial_seurat_WT.h5ad.

Thank you.

Wil