Re: MetaXcan

[Hae Kyung Im]

Please take a look at this tutorial to find the code you need https://lab-notes.hakyimlab.org/post/2022-06-10-qgt-training/index.html

On Sun, Sep 21, 2025 at 8:12 PM Ma, Lijiang <lijia...@mssm.edu> wrote:

Dear Dr. Hae Kyung lm,

I am a bioinformatician at Mount Sinai School of Medicine. I am trying to use the software MetaXcan to identify casual genes for disease by using GWAS summary statistics. It seems the script using MetaXcan

 such as the following is not working since MetaXcan.py is not in the software:

$ ./MetaXcan.py --gwas_folder /path/to/my/files --gwas_file_pattern ".*csv" \

--model_db_path my_model.db --covariance my_covariance.txt.gz \

--output_file /path/to/output \

The software contains MetaXcanUI.py instead. There is also SPrediXcan.py

May I know if MetaXcan.py is removed and I can only use SPrediXcan.py now? I will be greatly appreciated for your kind help if you could advise.

Thank you very much in advance for your kind help. I am looking forward to know your reply.

Regards,

Lijiang Ma