1. Programmatic access to bacterial regulatory networks with regutools
- Author
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Leonardo Collado-Torres, Joselyn Chávez, Carmina Barberena-Jonas, José Alquicira-Hernandez, Jesus E Sotelo-Fonseca, Heladia Salgado, and Alejandro Reyes
- Subjects
Statistics and Probability ,Computer science ,Gene regulatory network ,Biochemistry ,Bioconductor ,03 medical and health sciences ,0302 clinical medicine ,Transcriptional regulation ,Gene Regulatory Networks ,Molecular Biology ,Ecosystem ,030304 developmental biology ,Block (data storage) ,0303 health sciences ,Escherichia coli K12 ,business.industry ,Computational Biology ,Applications Notes ,Computer Science Applications ,DNA binding site ,Computational Mathematics ,Computational Theory and Mathematics ,Software engineering ,business ,Software ,030217 neurology & neurosurgery - Abstract
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.
- Published
- 2020
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