Open zji90 opened 4 years ago
I face the same issue on 10x dataset. The matrix size is around 5000 genes by 4000 samples. It is very slow.
Sorry it is not developed for 10X particularly. Given your size, 4000 with ~4000 sample penalized regressions with 5000 variables are needed for the analysis. I would image that will be very slow. We have a new method, called HIPPO, for 10X datasets. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02096-y Would you please take a look? I think that may be a better fit.
Thanks, Mengjie
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I face the same issue on 10x dataset. The matrix size is around 5000 genes by 4000 samples. It is very slow.
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Hi Dr. Mengjie, Thank you so much for your response. I will try the HIPPO.
Best, Wennan
Hi, I am testing VIPER on an 10x dataset with a few thousand cells. It has been taken around 24 hours but the program is still running. I wonder whether there is anything I can do to speed it up, like parallelization or change parameters? Thanks!