Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API

Area of Science:

• Bioinformatics
• Computational Biology
• Data Science

Background:

• The exponential growth of clinical, environmental, and biochemical data presents significant challenges in data management and analysis for precision medicine.
• Researchers need efficient tools to focus on research questions rather than complex data handling.

Purpose of the Study:

• To introduce Rcupcake, an R package designed to streamline data access, analysis, and interpretation from multiple databases.
• To facilitate the study of phenotype co-occurrence and prevalence across various data layers.

Main Methods:

• Developed an R package, Rcupcake, utilizing the BD2K PIC-SURE RESTful API.
• Implemented functions for querying, analyzing, and visualizing data from diverse sources.
• Included tools for phenotype co-occurrence and prevalence studies.

Main Results:

• Rcupcake provides a user-friendly interface for accessing and analyzing large-scale biomedical datasets.
• The package enables multi-layered data analysis, integrating phenome, exposome, and genome information.
• Demonstrated utility through two reproducible case studies.

Conclusions:

• Rcupcake empowers researchers by simplifying complex data management and analysis tasks.
• The package supports advanced research in precision medicine by facilitating the exploration of phenotype relationships across different data types.