Joselyn Chávez1, Carmina Barberena-Jonas2,3,4, Jesus E Sotelo-Fonseca2,3,4, José Alquicira-Hernández2,5,6, Heladia Salgado2, Leonardo Collado-Torres7, Alejandro Reyes8,9. 1. Departamento de Microbiología Molecular, Instituto de Biotecnología. 2. Programa de Genómica Computacional, Centro de Ciencias Genómicas. 3. Licenciatura de Ciencias Genómicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico 62210. 4. National Laboratory of Genomics for Biodiversity, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 36821, Mexico. 5. Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia. 6. Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia. 7. Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA. 8. Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA. 9. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
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.
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.
Authors: Wolfgang Huber; Vincent J Carey; Robert Gentleman; Simon Anders; Marc Carlson; Benilton S Carvalho; Hector Corrada Bravo; Sean Davis; Laurent Gatto; Thomas Girke; Raphael Gottardo; Florian Hahne; Kasper D Hansen; Rafael A Irizarry; Michael Lawrence; Michael I Love; James MacDonald; Valerie Obenchain; Andrzej K Oleś; Hervé Pagès; Alejandro Reyes; Paul Shannon; Gordon K Smyth; Dan Tenenbaum; Levi Waldron; Martin Morgan Journal: Nat Methods Date: 2015-02 Impact factor: 28.547
Authors: Michael Lawrence; Wolfgang Huber; Hervé Pagès; Patrick Aboyoun; Marc Carlson; Robert Gentleman; Martin T Morgan; Vincent J Carey Journal: PLoS Comput Biol Date: 2013-08-08 Impact factor: 4.475
Authors: Alberto Santos-Zavaleta; Heladia Salgado; Socorro Gama-Castro; Mishael Sánchez-Pérez; Laura Gómez-Romero; Daniela Ledezma-Tejeida; Jair Santiago García-Sotelo; Kevin Alquicira-Hernández; Luis José Muñiz-Rascado; Pablo Peña-Loredo; Cecilia Ishida-Gutiérrez; David A Velázquez-Ramírez; Víctor Del Moral-Chávez; César Bonavides-Martínez; Carlos-Francisco Méndez-Cruz; James Galagan; Julio Collado-Vides Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971