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Kyoko-wtnb / FUMA-webapp

Source code of FUMA GWAS web application
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FUMA-webapp, so that I could run FUMA on my laptop without internet connection? #6

Open jielab opened 4 years ago

jielab commented 4 years ago

Hi, Previously I have user FUMA a little bit, by submitting my GWAS to the FUMA web server. And I have been wishing that you guys could release a version that I could install locally.

So, is FUMA-webapp something that I have been hoping for, something that I could download and set up and run on my local computer? That would be really awesome!

Best regadrs, jie

Kyoko-wtnb commented 4 years ago

Hi Jie,

Yes, I'm working on it! I am creating python stand-alone version of FUMA, I just need to find a time to test and documents them. Currently, I cannot work on FUMA full time, it might take bit longer than I planned... But I'll do my best!

Best, Kyoko

jielab commented 4 years ago

Thanks, Kyoko!

I recently read a Bioinformatics paper "the open targets post-GWAS analysis pipeline"（https://github.com/Ensembl/postgap）. Don't know if they are developing something similar as FUMA.

After I finished running a GWAS, before I go to functional mapping, there are some general steps needed in between. For example, the following steps are what I usually do after I run a GWAS, or after I download a GWAS from a public space.

  1. use qqman() R package to make a Manhattan plot.

  2. manually extract known genetic loci of this trait from GWAS catalog and then compare BETA and EAF with my GWAS, by a R script

  3. find known loci from GWAS catalog and then use plink --clump to identify independent and novel loci.

  4. ran locuszoom on loci of interest.

  5. run VEP on the variants of interest.

  6. FUMA or network analysis etc.

Can you please comment on this flow? I guess that I still need to do the above tasks manually, one by one.

BTW, if you need someone with Python experience, maybe I could recommend you a Bioinformatics major student from UCSD who is eager to learn and develop.

Best regards, Jie

Kyoko-wtnb commented 4 years ago

Hi Jie,

I think that's what generally people do for post-GWAS. Some of the steps, like overlap with GWAS catalog or creating manhattan plot is part of FUMA but I can imagine doing it by yourself gives you more flexibility.

Thank you for your very generous gesture, I will see how far I can go in the next couple of months.

Best, Kyoko

jielab commented 3 years ago

Dear Kyoko:

Don't know if there is progress on making a stand-alone version of FUMA.

Best regards, Jie

alisonrocco commented 2 years ago

Hi Kyoko,

Is there any update on the stand-alone version of FUMA? My lab has run into issues with the file size limitation while using the web application and would like to install FUMA locally on our University's research computing cluster.

Sincerely, Alison