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.

中文翻译：

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使用regutools以编程方式访问细菌监管网络。

RegulonDB近二十年来从数百个实验中收集，协调和集中了数据，被认为是大肠杆菌K12转录调控的参考点。在这里，我们介绍了regutools R软件包，以方便在计算生物学中对RegulonDB数据进行编程访问。regutools使研究人员可以通过自动查询向RegulonDB编写可重复的工作流。所述regutools包充当之间的桥梁RegulonDB数据和Bioconductor的供电由其它通过复用数据结构的生态系统和统计学方法生物导体包装。我们通过分析转录因子DNA结合位点和RegulonDB的转录调控网络，证明了regutools与Bioconductor的整合。我们预计，regutools将成为我们进步的有用组成部分，以进一步了解基因调控网络。