VIPER very slow on 10x dataset

[zji90]

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]

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

[ChenMengjie]

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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________________________________ From: changwn <[email protected]> Sent: Thursday, January 7, 2021 12:09 PM To: ChenMengjie/VIPER <[email protected]> Cc: Subscribed <[email protected]> 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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#3 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AD7DL3KQNK5TFUAQRGWHLN3SYX2ENANCNFSM4IW34PJQ>.

[changwn]

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

Best,
Wennan