Paparozzi Veronica, Nardini Christine
Institute for Applied Mathematics (IAC) "Mauro Picone", National Research Council (CNR), Rome 00185, Italy.
Bioinform Adv. 2024 Oct 3;4(1):vbae148. doi: 10.1093/bioadv/vbae148. eCollection 2024.
We present , an R package able to perform , , and 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 , , and . Exemplar data (i.e. SBML files) are extracted from Reactome.
The 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).
我们展示了tidysbml，这是一个R包，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，最高到第3级）文档中执行模型解析、数据提取和数据检索，以便轻松访问和处理丰富的生物信息。由于其输出格式，该包便于数据操作，能够构建可管理的自定义网络并进行分析，还能借助诸如dplyr、tidyr和ggplot2等R包进行数据检索。示例数据（即SBML文件）取自Reactome。
tidysbml R包根据CC BY 4.0许可进行分发，可在Bioconductor（https://bioconductor.org/packages/tidysbml）和GitHub（https://github.com/veronicapaparozzi/tidysbml）上公开获取。
