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

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The new R/Bioconductor package, pgxRpi, simplifies accessing genomic data via the Beacon v2 API. It enables efficient data retrieval, exploration, and analysis across multiple resources, enhancing genomic discovery.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Science

Background:

  • The Global Alliance for Genomics and Health (GA4GH) established the Beacon v2 specification for standardized genomic and phenotypic data discovery.
  • Beacon v2 promotes secure, federated data sharing and interoperability across genomic resources.
  • Progenetix is a reference implementation of Beacon v2, providing access to large-scale cancer genomic mutation data.

Purpose of the Study:

  • To introduce pgxRpi, an open-source R/Bioconductor package.
  • To provide a streamlined interface to the Progenetix Beacon v2 REST API for efficient genomic data retrieval.
  • To enable flexible data exploration, interpretation, and processing through integrated visualization and analysis functions.

Main Methods:

  • Development of an R/Bioconductor package (pgxRpi).
  • Implementation of a streamlined interface to the Progenetix Beacon v2 REST API.
  • Integration of visualization and analysis functions for queried genomic data.

Main Results:

  • pgxRpi facilitates efficient and flexible genomic data retrieval via the Beacon v2 API.
  • The package supports interoperable data access across multiple Beacon-enabled resources beyond Progenetix.
  • Integrated functions allow users to explore, interpret, and process queried genomic data effectively.

Conclusions:

  • pgxRpi enhances data-driven discovery in genomics by leveraging the Beacon v2 standard.
  • The package offers a powerful tool for researchers to access and analyze distributed genomic datasets.
  • pgxRpi is freely available, promoting open-source collaboration in genomic data science.