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Programmatic access to bacterial regulatory networks with regutools


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

Type Journal
ISBN 1367-4811 (Electronic) 1367-4803 (Linking)
Authors Chavez, J.; Barberena-Jonas, C.; Sotelo-Fonseca, J. E.; Alquicira-Hernandez, J.; Salgado, H.; Collado-Torres, L.; Reyes, A.
Responsible Garvan Author Jose Alquicira Hernandez
Publisher Name Bioinformatics
Published Date 2020-08-31
Published Volume 36
Published Issue 16
Published Pages 4532-4534
Status Published in-print
DOI 10.1093/bioinformatics/btaa575
URL link to publisher's version