Speed of Cell-Cell interaction analysis on scRNA-seq data
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Entering edit mode
12 months ago
miyeok • 0

Hi all,

i am trying to perform Cell-Cell interaction analysis on scRNA-seq data processed by Seurat. And I'm using Cellchat for analysis package, but it is taking forever, I have about 10k cells in each samples. and total sample numbers are 8. By the way, my computer have 12 CPU core num. If there is a more faster way or package of cell-cell interaction analysis (LR-interaction)?

Any anwsers would be appreciated.

Cellchat scRNA-seq Seurat • 530 views
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Entering edit mode
9 days ago
t.foskolos • 0

You can try nichenet, specifically i am trying to setup multinichenet and it allows for parallelization based on the cores that you have. (though its a bit different than cellchat)

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Entering edit mode
7 days ago
gglim ▴ 160

Have you tried this command ? future::plan("multiprocess", workers = num_of_cores)

I found it in my previous script but I'm not sure if it worked.

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