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How to change min.gene.per.cell #117

Open Rayan21100 opened 4 months ago

Rayan21100 commented 4 months ago

Hi,

I'm analyzing single-cell spatial transcriptomic, more specifically CosMx data base. In this database, I don't have the whole genome but only 960 genes. I would have liked to use copykat but the problem is that most of my cells get filtered out because they express less genes than what is specified in min.gene.per.cell:

[1] "960 genes, 97907 cells in raw data"
[1] "filtered out 82746 cells with less than min.gene.per.cell; remaining 15448 cells"

I think they get filtered out because I have only 960 genes, is there a way to lower the min.gene.per.cell ? I can't find anywhere a way to do it...

Thank you in advance !

yitengfei120011 commented 2 weeks ago

I have the same problem, I want to keep all the cells I input, because I have done cell filtering in scanpy.