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引用次数: 0
摘要
摘要：我们介绍的 tidysbml 是一个 R 软件包，它能够以表格数据结构（即 R 数据框）从系统生物学标记语言（SBML）文档（最高 3 级）中提取区系、物种和反应数据，从而轻松访问和处理丰富的生物信息。得益于其输出格式，该软件包方便了数据操作，可通过 igraph、RCy3 和 biomaRt 等 R 软件包管理自定义网络的构建和分析，以及数据检索。 示例数据（即 SBML 文件）从 Reactome.Availability 和实现中提取：tidysbml R 软件包以 CC BY 4.0 许可发布，可在 Bioconductor (https://bioconductor.org/packages/tidysbml) 和 GitHub (https://github.com/veronicapaparozzi/tidysbml) 上公开获取。
tidysbml: R/Bioconductor package for SBML extraction into dataframes.
Summary: We present tidysbml, an R package able to perform compartments, species, and reactions data extraction from Systems Biology Markup Language (SBML) documents (up to Level 3) in tabular data structures (i.e. R dataframes) to easily access and handle the richness of the biological information. Thanks to its output format, the package facilitates data manipulation, enabling manageable construction, and therefore analysis, of custom networks, as well as data retrieval, by means of R packages such as igraph, RCy3, and biomaRt. Exemplar data (i.e. SBML files) are extracted from Reactome.
Availability and implementation: The tidysbml R package is distributed under CC BY 4.0 License and can be found publicly available in Bioconductor (https://bioconductor.org/packages/tidysbml) and on GitHub (https://github.com/veronicapaparozzi/tidysbml).
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