介绍GalaxyR：一个易于使用的Galaxy API的R语言实现

摘要(中文译文)

标准化、可及性和可重复性仍然是数据密集型科学研究中持续存在的挑战。Galaxy平台通过提供基于网络的执行、共享和发布计算工作流的环境来应对这些问题，然而程序化访问在很大程度上仍以Python生态系统为中心，通过BioBlend实现。在此，我们介绍GalaxyR，一个原生R包，为Galaxy应用程序编程接口提供全面且结构化的接口。GalaxyR使用户能够直接在R环境中管理历史记录、上传和检索数据、执行工具和工作流、监控作业以及检查结果。通过将Galaxy的可扩展计算基础设施与R广泛采用的数据分析生态系统相集成，GalaxyR促进了自动化、可重复且资源高效的工作流，而无需本地高性能计算资源。该包支持基于HTTPS和FTP的数据传输、稳健的历史记录和数据集管理，以及跨Galaxy实例的程序化工作流编排。一个应用示例展示了使用GalaxyR对基于无人机的激光扫描数据进行大规模处理，其中计算密集型的树级分割被委托给Galaxy基础设施，而工作流控制和预处理则在R中通过几行代码完成。因此，GalaxyR为R用户弥合了一个关键缺口，显著扩展了对基于Galaxy的分析的访问，并使得跨生物信息学、生态学、遥感及相关数据驱动学科的可扩展、可重复研究成为可能。

Abstract

Standardisation, accessibility, and reproducibility remain persistent challenges in data‑intensive scientific research. The Galaxy platform addresses these issues by providing a web-based environment for executing, sharing, and publishing computational workflows, yet programmatic access has been largely centred on the Python ecosystem through BioBlend. Here, we introduce GalaxyR, a native R package that provides a comprehensive and structured interface to the Galaxy application programming interface. GalaxyR enables users to manage histories, upload and retrieve data, execute tools and workflows, monitor jobs, and inspect results directly from within the R environment. By integrating Galaxy's scalable computational infrastructure with R's widely adopted data analysis ecosystem, GalaxyR facilitates automated, reproducible, and resource‑efficient workflows without requiring local high‑performance computing resources. The package supports both HTTPS‑ and FTP‑based data transfer, robust history and dataset management, and programmatic workflow orchestration across Galaxy instances. An application example demonstrates the use of GalaxyR for large-scale processing of drone-based laser scanning data, where computationally intensive tree‑level segmentation was delegated to the Galaxy infrastructure, while workflow control and preprocessing were handled in R within a few lines of code. GalaxyR thus bridges a critical gap for R users, significantly expanding access to Galaxy‑based analyses and enabling scalable, reproducible research across bioinformatics, ecology, remote sensing, and related data-driven disciplines.

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