GP2 ❤️ Open Science 😍
Last Updated: June 2025
This repository contains all analyses for the manuscript titled "Sex-stratified analysis of the potential association between PGLYRP2 rs892145 variant and Parkinson’s disease across diverse ancestral populations".
- Results were generated using
- GP2 data release 9 (controlled-tier access; DOI: 10.5281/zenodo.14510099
- AMP-PD v3.0 (controlled-tier access)
analyses/
├── AMPPD
│ └── 00_PGLYRP2_singlegene-analysis_AMPPD
└── GP2
└── 00_PGLYRP2_singlegene-analysis_GP2.ipynb
| Directory | Notebook | Description |
|---|---|---|
| AMPPD/ | 00_PGLYRP2_singlegene-analysis_AMPPD.ipynb |
Analyses of AMP-PD whole-genome sequencing data |
| GP2/ | 00_PGLYRP2_singlegene-analysis_GP2.ipynb |
Analyses of GP2 genotyped imputed data across ancestries |
All individual-level data have been removed, including sample IDs and identifiers. Sensitive paths have been cleared. Notebooks have been saved as .ipynb files for easy sharing while ensuring compliance with data privacy standards.
| Software/Tool | Version | Resource URL | RRID | Notes |
|---|---|---|---|---|
| Python | 3.10 | http://www.python.org/ | RRID:SCR_008394 | pandas; numpy; forestplot; matplotlib used for general data wrangling/plotting/analysis |
| Jupyter Notebook | 4.3 | https://jupyter.org | RRID:SCR_018315 | used to keep record of the analysis pipeline |
| PLINK | 1.9 | https://www.cog-genomics.org/plink/ | RRID:SCR_001757 | used for LD calculations |
| PLINK | 2.0 | https://www.cog-genomics.org/plink/2.0/ | RRID:SCR_001757 | used for association analysis |
| BCFTOOLS | 1.21 | https://github.com/samtools/bcftools | RRID:SCR_005227 | used for manipulating, analyzing, and calling genetic variants |
| ANNOVAR | 2019Oct24 | https://annovar.openbioinformatics.org/ | RRID:SCR_012821 | used for annotation of genetic variants |
| RVTESTS | 2.1 | https://github.com/zhanxw/rvtests/ | RRID:SCR_007639 | used for burden analysis |
| R | 4.4.2 | http://www.r-project.org/ | RRID:SCR_001905 | used for interaction analyses |
| Inkscape | 1.4.2 | https://inkscape.app/ | RRID:SCR_014479 | used for figure composition |