Error using sparse matrix to run SCENIC

[yilingmialiu]

Hi,

I have a big dataset with 17K genes X 270K cells, I'm wondering if I can run the SCENIC workflow using sparsematrix, as in dgCMatrix? I ran into errors right from the first step: geneFiltering. It seems not realistic to covert this huge dataset to dense matrix.

Thanks, Mia

[zh-zhang1984]

I also have the same problem when running the SCENIC

[jingjiai]

I also have the same problem. I extracted 1000 cells randomly to analyze as the paper did, entitled "SCENIC : single-cell regulatory network inference and clustering", to solve this problem.