Table 2.

Summary of the goals and outcomes of each of the hackathon projects.

Topic	Project title	Goal	Outcome	Links to code or applications
GWAS-level and post-GWAS analyses	Project 1: Post-GWAS analysis	Develop a pipeline for some common post-GWAS follow-up analyses	GREML-LDMS and PRS analyses coded and tested on AMP PD data	Github: https://github.com/ipdgc/GP2-post-GWAS-analysis Zenodo: 10.5281/zenodo.6477900
	Project 2: Pathway and cell-type enrichment pipeline	Develop a pipeline for investigating pathway and cell-type enrichment from GWAS summary statistics	Code for gene set enrichment with WebGestaltR on Terra as well as formatting summary statistics for FUMA	Github: https://github.com/ipdgc/GP2-pathway-enrichment-pipeline Zenodo: 10.5281/zenodo.6477914
Downstream analyses of genetic variation	Project 3: Colocalization pipeline	Develop a pipeline for colocalization analysis	Code for colocalization and visualization with the coloc and eQTpLot R packages	Github: https://github.com/ipdgc/Colocalization-Pipeline Zenodo: 10.5281/zenodo.6477921
	Project 4: Network generation and visualization pipeline	Develop a pipeline that generates and visualizes gene regulatory networks	Code for generating Leiden networks with eQTL and genetic data with the leidenalg python package	Github: https://github.com/ipdgc/GP2-network-generation Zenodo: 10.5281/zenodo.6477923
	Project 5: Variant interaction pipeline	Develop a pipeline that investigates variant interaction	Code for data prep with Plink1.9 and ANNOVAR, as well as interaction tests with glm in R	Github: https://github.com/ipdgc/GP2-Variant-Interaction-Pipeline Zenodo: 10.5281/zenodo.6477931
Data visualization	Project 6: GP2 cohort tracker visualization	Develop a dashboard for tracking and investigating the progress of cohort integration for GP2	Both an internal and external dashboard can be used to investigate information about participating GP2 cohorts	Application: https://gp2.org/cohort-dashboard/
	Project 7: PD GWAS Loci Browser expansions	Expand the functionality of the PD GWAS Loci Browser	Locus zoom plots for conditional analyses, power calculations, violin plots for expression data, and user statistics were added to the Loci Browser	Application: https://pdgenetics.shinyapps.io/GWASBrowser/ RRID: SCR_022188
	Project 8: Visualization of longitudinal UPDRS/HY scores	Visualize longitudinal clinical measures of PD	Python Streamlit application for visualizing UPDRS and HY score progression	Application: https://share.streamlit.io/tantar/hack/main/GP2_data_visualization.py RRID: SCR_022187
	Project 9: Visualize longitudinal and cross-sectional variant effects	Visualize longitudinal and cross-sectional variant effects from GWAS	Code for running an R shiny application that visualizes variant effects across cohorts	Github: https://github.com/ipdgc/GP2-visualize-longitudinal-variant-effects Zenodo: 10.5281/zenodo.6477935

Access to the code or applications developed during the hackathon is included in the “Links to Code or Applications” column.