tidysbml: R/Bioconductor package for SBML extraction into dataframes.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Bioinformatics advances Pub Date : 2024-10-03 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae148
Veronica Paparozzi, Christine Nardini
{"title":"tidysbml: R/Bioconductor package for SBML extraction into dataframes.","authors":"Veronica Paparozzi, Christine Nardini","doi":"10.1093/bioadv/vbae148","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>We present <i>tidysbml</i>, an R package able to perform <i>compartments</i>, <i>species</i>, and <i>reactions</i> 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 <i>igraph</i>, <i>RCy3</i>, and <i>biomaRt</i>. Exemplar data (i.e. SBML files) are extracted from Reactome.</p><p><strong>Availability and implementation: </strong>The <i>tidysbml</i> 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).</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae148"},"PeriodicalIF":2.4000,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11479578/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbae148","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

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).

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
tidysbml:用于将 SBML 提取到数据帧中的 R/Bioconductor 软件包。
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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
CiteScore
1.60
自引率
0.00%
发文量
0
期刊最新文献
MultiOmicsIntegrator: a nextflow pipeline for integrated omics analyses. mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data. Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics. AAclust: k-optimized clustering for selecting redundancy-reduced sets of amino acid scales. Exon nomenclature and classification of transcripts database (ENACTdb): a resource for analyzing alternative splicing mediated proteome diversity.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1