- Pleiotropic Locus Exploration and Interpretation using Optimal test
pleio is a command line tool for performinig meta-analysis of multiple GWAS summary statistics.
In order to download pleio, you should clone this repository via the command
git clone git://github.com/hanlab-SNU/pleio.git
cd pleio
In order to run pleio, the following python dependencies must be installed in your system.
- python >= 3.7.4
- pandas >= 1.0.4
- numpy = v.1.16.4
- scipy >= v.1.4.1
To install Python dependencies, you need to install an Anaconda python distribution from LINK. After installing Anaconda, run the following command to create an environment with pleio's dependencies.
conda env create -f environment.yml
conda activate pleio
Once the above has completed, you can run the following command:
./pleio -h
You can update to the newest version of PLEIO using git. First, navigate to your pleio/ directory (e.g., cd pleio), then run
git pull
If PLEIO is up to date, you will see
Already up-to-date.
otherwise, you will see git output similar to
remote: Enumerating objects: 9, done.
remote: Counting objects: 100% (9/9), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 6 (delta 4), reused 5 (delta 3), pack-reused 0
Unpacking objects: 100% (6/6), done.
From git://github.com/hanlab-SNU/pleio
e065a06..14c3399 master -> origin/master
Updating e065a06..14c3399
Fast-forward
README.md | 2 +-
ldsc_preprocess | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
If you want to try a joint analysis of 18 characteristics of cardiovascular diseases using the PLEIO framework, please use the following link
If you use the software, please cite
Cue Hyunkyu Lee., Huwenbo Shi., Bogdan Pasaniuc., Eleazar Eskin., Buhm Han. A method to map and interpret pleiotropic loci using summary statistics of multiple traits. bioRxiv 2020.06.16.155879; doi: https://doi.org/10.1101/2020.06.16.155879
Issues with PLEIO? Email cuelee@snu.ac.kr
This project has no license currently.
Cue Hyunkyu Lee ( Seoul National University )