pgxRpi

pgxRpi provides an R/Bioconductor interface to the Progenetix Beacon v2 REST API for retrieving, visualizing, and analyzing genomic mutation data from curated oncogenomic profiles.

Key Features:

• Beacon v2 API Access: Implements a streamlined interface to the Progenetix Beacon v2 REST API for efficient genomic data retrieval.
• Data Visualization: Provides integrated visualization functions to explore and interpret queried genomic data.
• Cross-Resource Interoperability: Supports data access across multiple Beacon-enabled resources beyond Progenetix through the flexibility of the Beacon v2 standard.
• Data Analysis: Includes analysis functions for processing queried genomic and phenotypic data.

Scientific Applications:

• Oncogenomic Data Retrieval: Enables access to curated genomic mutation data across diverse cancer types from the Progenetix database.
• Federated Genomic Discovery: Facilitates secure, interoperable data sharing and discovery across genomic resources implementing the GA4GH Beacon v2 specification.
• Cancer Genomics Research: Supports large-scale genomic data integration and data-driven discovery in cancer genomics through standardized data models.

Methodology:

The package wraps the Progenetix REST API built upon the Beacon v2 protocol established by the Global Alliance for Genomics and Health (GA4GH).