cailab-tamu / scTenifoldKnk

R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
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Question: How to run scTenifoldKnk on one cluster #18

Open abedkurdi opened 2 years ago

abedkurdi commented 2 years ago

Hello sir, I would like to ask if you can guide me on how to run your tool on one cluster. Am I supposed to remove genes from the subsetted cluster? I tried to run the tool using the normalized count (using Seurat log-normalize method) for the subsetted cluster, but it is not giving me any significant results. I also tried to run it on the counts, it is taking a lot of time (~15 hours) and it fails by returning the following error: Error in dim(mat) <- new_modes : the dims contain missing values .

I appreciate any help and guidance. Thank you in advance! Abed.