GP2 ❤️ Open Science 😍
Last Updated: November 2023
This is the online repository for the manuscript titled "SH3GL2 variants and the risk for Parkinson’s disease in diverse ancestry populations". This study focuses on exploring the role of SH3GL2 in existing PD/control datasets from the AMP-PD and GP2 initiatives.
All data was using release 5 GP2 data (access-controlled via single-sign on amp-pd.org).
- Languages: Python, bash, and R
Notebooks | Description |
---|---|
SH3GL2_AMP_PD | SH3GL2 variants screening in AMP-PD data v3.0 - European ancestry |
SH3GL2_GP2_AAC | SH3GL2 variants screening in GP2 data (release 5) - African admixed ancestry |
SH3GL2_GP2_AFR | SH3GL2 variants screening in GP2 data (release 5) - African ancestry |
SH3GL2_GP2_AJ | SH3GL2 variants screening in GP2 data (release 5) - Ashkenazi Jewish ancestry |
SH3GL2_GP2_AMR | SH3GL2 variants screening in GP2 data (release 5) - Amerindian ancestry |
SH3GL2_GP2_CAS | SH3GL2 variants screening in GP2 data (release 5) - Central Asian ancestry |
SH3GL2_GP2_EAS | SH3GL2 variants screening in GP2 data (release 5) - East Asian ancestry |
SH3GL2_GP2_EUR | SH3GL2 variants screening in GP2 data (release 5) - European ancestry |
SH3GL2_GP2_FIN | SH3GL2 variants screening in GP2 data (release 5) - Finnish ancestry |
SH3GL2_GP2_MDE | SH3GL2 variants screening in GP2 data (release 5) - Middle Eastern ancestry |
SH3GL2_GP2_SAS | SH3GL2 variants screening in GP2 data (release 5) - South Asian ancestry |
(pending publication)
Software | Version(s) | Resource URL | RRID | Notes |
---|---|---|---|---|
ANNOVAR | 2020-06-08 | http://www.openbioinformatics.org/annovar/ | RRID:SCR_012821 | refGene; avsnp150; ljb26_all; gnomad312_genome; used for annotation |
PLINK | 1.7 and 1.9 and 2.0 | http://www.nitrc.org/projects/plink | RRID:SCR_001757 | used for genetic analyses |
Python Programming Language | 3.8 and 3.9 | http://www.python.org/ | RRID:SCR_008394 | pandas; numpy; seaborn; matplotlib; statsmodel; used for general data wrangling/plotting/analyses |
R Project for Statistical Computing | 4.2 | http://www.r-project.org/ | RRID:SCR_001905 | tidyverse; dplyr; tidyr; ggplot; data.table; used for general data wrangling/plotting/analyses |