Zhao Hangjia, Baudis Michael
Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland.
Computational Oncogenomics Group, Swiss Institute of Bioinformatics, Zurich 8057, Switzerland.
Bioinform Adv. 2025 Jul 16;5(1):vbaf172. doi: 10.1093/bioadv/vbaf172. eCollection 2025.
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.
We present , 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, offers integrated visualization and analysis functions, enabling users to explore, interpret, and process queried data effectively. Leveraging the flexibility of the Beacon v2 standard, extends beyond Progenetix, supporting interoperable data access across multiple Beacon-enabled resources, thereby enhancing data-driven discovery in genomics.
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.
全球基因组学与健康联盟（GA4GH）制定的Beacon v2规范，由用于基因组和表型数据发现的标准化框架及数据模型组成。通过实现安全的联邦数据共享，它促进了基因组资源之间的互操作性。Progenetix作为Beacon v2的参考实现，例证了其在大规模基因组数据整合方面的潜力，提供了对多种癌症类型的基因组突变数据的开放访问。
我们展示了一个开源的R/Bioconductor包，它为Progenetix Beacon v2 REST API提供了一个简化的接口，便于高效灵活地检索基因组数据。除了数据访问，该包还提供了集成的可视化和分析功能，使用户能够有效地探索、解释和处理查询到的数据。利用Beacon v2标准的灵活性，该包超越了Progenetix，支持跨多个启用Beacon的资源进行可互操作的数据访问，从而增强了基因组学中数据驱动的发现。
该包可在Bioconductor上根据Artistic-2.0许可免费获取（https://doi.org/10.18129/B9.bioc.pgxRpi），其源代码在GitHub上积极维护（https://github.com/progenetix/pgxRpi）。在包的 vignettes中提供了全面的使用说明和示例工作流程，可在https://github.com/progenetix/pgxRpi/tree/devel/vignettes获取。
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