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ChenMengjie / VIPER

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VIPER very slow on 10x dataset #3

Open zji90 opened 4 years ago

zji90 commented 4 years ago

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!

changwn commented 3 years ago

I face the same issue on 10x dataset. The matrix size is around 5000 genes by 4000 samples. It is very slow.

ChenMengjie commented 3 years ago

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

From: changwn notifications@github.com Sent: Thursday, January 7, 2021 12:09 PM To: ChenMengjie/VIPER VIPER@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [ChenMengjie/VIPER] VIPER very slow on 10x dataset (#3)

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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changwn commented 3 years ago

Hi Dr. Mengjie, Thank you so much for your response. I will try the HIPPO.

Best, Wennan