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.