pgxRpi: an R/bioconductor package for user-friendly access to the Beacon v2 API.

Abstract

Motivation: The Beacon v2 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 Beacon v2 reference implementation, exemplifies its potential for large-scale genomic data integration, offering open access to genomic mutation data across diverse cancer types.

Results: We present pgxRpi, an open-source R/Bioconductor package that provides a streamlined interface to the Progenetix Beacon v2 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 v2 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 (https://doi.org/10.18129/B9.bioc.pgxRpi), with actively maintained source code on GitHub (https://github.com/progenetix/pgxRpi). Comprehensive usage instructions and example workflows are provided in the package vignettes, available at https://github.com/progenetix/pgxRpi/tree/devel/vignettes.