UKBAnalytica: an integrated R package for scalable phenotyping and reproducible epidemiological analysis within the UK Biobank Research Analysis Platform

UKBAnalytica is an extensible R package designed for analyzing data from UK Biobank, which contains data from approximately 500,000 participants. The package includes 52 predefined baseline variables and a library of 331 curated disease definitions based on ICD-10, ICD-9, self-reported conditions, death registry records, algorithmically defined outcomes, and OPCS-4 procedure codes. UKBAnalytica distinguishes prevalent and incident cases, constructs follow-up time, and generates analysis-ready survival datasets. The package provides integrated modules for epidemiological analysis, omics analysis, and machine-learning-based modeling. The practical utility of the package was demonstrated through a case study on chronic obstructive pulmonary disease (COPD) proteomics. The findings align with previously reported conclusions, confirming the robustness and reliability of the analytical framework.