PheTK

PheTK streamlines phenome-wide association study (PheWAS) analysis for large-scale biobank data using multithreading to efficiently handle biobank-scale datasets.

Key Features:

• Data Extraction: Extracts data from OMOP databases and Hail matrix tables.
• PheWAS Analysis: Supports PheWAS analysis for both phecode version 1.2 and phecodeX.
• Multithreading: Uses multithreading to efficiently process biobank-scale data, completing workflows in 64% less time than the R PheWAS package.
• Visualization: Provides tools for visualization of PheWAS results.

Scientific Applications:

• Large-Scale PheWAS: Enables phenome-wide association studies utilizing longitudinal electronic health record (EHR) data in large cohorts.
• Biobank Data Analysis: Supports analysis on biobank platforms including the All of Us Researcher Workbench and the UK Biobank Research Analysis Platform.

Methodology:

PheTK implements multithreading for parallel processing and supports extraction of data from OMOP databases and Hail matrix tables for PheWAS analysis with phecode version 1.2 and phecodeX.