EMMA：一个用于自动化跟踪功能富集分析中元数据的R/Bioconductor包
EMMA: an R/Bioconductor package to automate tracking of metadata in functional enrichment analyses
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中文总结 AI 辅助
EMMA是一个R/Bioconductor包，自动捕获功能富集分析中的来源元数据，如软件版本和参数，以提高可重复性和透明度。
中文摘要 AI 辅助
摘要：功能富集分析（FEA）是解释高通量组学数据的一种广泛使用的方法。然而，关键的方法学细节，如软件版本、分析参数和注释数据库版本等，往往报告不完整，限制了富集分析的可重复性和透明度，并使评估潜在有问题的方法学选择变得复杂。在此，我们介绍EMMA，一个R/Bioconductor包，它与现有的FEA工具集成，并在分析运行期间自动捕获来源元数据，如注释元数据、软件版本和参数。我们的包提供了访问和导出所记录元数据的实用程序，以促进透明报告并保留可重复富集分析所需的来源信息。这还使得在保持与现有Bioconductor工作流兼容的同时，能够对结果进行审计。可用性和实现：EMMA在MIT许可证下可在Bioconductor上获得（https://bioconductor.org/packages/EMMA），其开发版本也可在GitHub上获得（https://github.com/imbeimainz/EMMA）。
英文摘要
Summary: Functional enrichment analysis (FEA) is a widely used approach for interpreting high-throughput omics data. However, essential methodological details, such as software versions, analysis parameters, and annotation database releases among others, are often incompletely reported, limiting the reproducibility and transparency of enrichment analyses and complicating the assessment of potentially problematic methodological choices. Here we present EMMA, an R/Bioconductor package that integrates with existing FEA tools and automatically captures provenance metadata, such as annotation metadata, software version, and parameters, during the analysis runtime. Our package provides utilities for accessing and exporting the recorded metadata to facilitate transparent reporting and preserve provenance required for reproducible enrichment analyses. This also enables auditing of the results while remaining compatible with existing Bioconductor workflows. Availability and implementation: EMMA is available on Bioconductor under the MIT license (https: //bioconductor.org/packages/EMMA), with its development version also available on GitHub (https: //github.com/imbeimainz/EMMA).
发表机构
- University Medical Center Mainz（美因茨大学医学中心）
- Research Center for Immunotherapy (FZI) Mainz（美因茨免疫治疗研究中心）
机构由 AI 辅助整理，请以论文原文为准。
