Error using sparse matrix to run SCENIC

aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

http://scenic.aertslab.org

GNU General Public License v3.0

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Error using sparse matrix to run SCENIC #160

Open yilingmialiu opened 3 years ago

yilingmialiu commented 3 years ago

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 commented 2 years ago

I also have the same problem when running the SCENIC

jingjiai commented 2 years ago

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.