使用 regutools 实现对细菌调控网络的编程访问。
Programmatic access to bacterial regulatory networks with regutools.
机构信息
Departamento de Microbiología Molecular, Instituto de Biotecnología.
Programa de Genómica Computacional, Centro de Ciencias Genómicas.
出版信息
Bioinformatics. 2020 Aug 15;36(16):4532-4534. doi: 10.1093/bioinformatics/btaa575.
SUMMARY
RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools gives researchers the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.
AVAILABILITY AND IMPLEMENTATION
regutools is an R package available through Bioconductor at bioconductor.org/packages/regutools.
摘要
RegulonDB 近二十年来收集、协调和集中了数百项实验的数据，被认为是大肠杆菌 K12 转录调控的参考点。在这里，我们提出了 regutools R 包，以方便在计算生物学中对 RegulonDB 数据进行编程访问。regutools 为研究人员提供了使用自动查询到 RegulonDB 的可重复工作流程的可能性。regutools 包通过重复使用由其他 Bioconductor 包提供的数据结构和统计方法，在 RegulonDB 数据和 Bioconductor 生态系统之间架起了桥梁。我们通过分析来自 RegulonDB 的转录因子 DNA 结合位点和转录调控网络来展示 regutools 与 Bioconductor 的集成。我们预计，regutools 将成为我们进一步了解基因调控网络的有用构建块。
可用性和实现
regutools 是一个 R 包，可通过 Bioconductor 在 bioconductor.org/packages/regutools 上获得。
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