pgxRpi: an R/Bioconductor package for user-friendly access to the Beacon API
Hangjia Zhao and Michael Baudis¶
Bioinform Adv. 2025 Jul 16;5(1):vbaf172¶
- doi: 10.1093/bioadv/vbaf172
- PMID: 40761325
Abstract: The Beacon specification, established by the Global Alliance for Genomics and Health (GA4GH), consists of a standardized framework and data models for genomic and phenotypic data discovery. By enabling secure, federated data sharing, it fosters interoperability across genomic resources. Progenetix, a reference implementation of Beacon, exemplifies its potential for large-scale genomic data integration, offering open access to genomic mutation data across diverse cancer types. Here we present pgxRpi, an open-source R/Bioconductor package that provides a streamlined interface to the Progenetix Beacon REST API, facilitating efficient and flexible genomic data retrieval. Beyond data access, pgxRpi offers integrated visualization and analysis functions, enabling users to explore, interpret, and process queried data effectively. Leveraging the flexibility of the Beacon standard, pgxRpi extends beyond Progenetix, supporting interoperable data access across multiple Beacon-enabled resources, thereby enhancing data-driven discovery in genomics.
Availability and Implementation: pgxRpi is freely available under the Artistic-2.0 license from Bioconductor, with actively maintained source code on GitHub. Comprehensive usage instructions and example workflows are provided in the package vignettes.