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message: 'To cite package "regutools" in publications use:'
type: software
license: Artistic-2.0
title: 'regutools: regutools: an R package for data extraction from RegulonDB'
version: 1.17.0
doi: 10.18129/B9.bioc.regutools
abstract: 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
  provides researchers with 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.
authors:
- family-names: Chavez
  given-names: Joselyn
  email: joselynchavezf@gmail.com
  orcid: https://orcid.org/0000-0002-4974-4591
- family-names: Barberena-Jonas
  given-names: Carmina
  email: car.barjon@gmail.com
  orcid: https://orcid.org/0000-0001-7413-638X
- family-names: Sotelo-Fonseca
  given-names: Jesus E.
  email: jemilianosf@gmail.com
  orcid: https://orcid.org/0000-0003-1600-2396
- family-names: Collado-Torres
  given-names: Leonardo
  email: lcolladotor@gmail.com
  orcid: https://orcid.org/0000-0003-2140-308X
- family-names: Reyes
  given-names: Alejandro
  email: alejandro.reyes.ds@gmail.com
  orcid: https://orcid.org/0000-0001-8717-6612
preferred-citation:
  type: manual
  title: 'regutools: an R package for data extraction from RegulonDB'
  authors:
  - family-names: Chávez
    given-names: Joselyn
  - family-names: Barberena-Jonas
    given-names: Carmina
    email: car.barjon@gmail.com
    orcid: https://orcid.org/0000-0001-7413-638X
  - family-names: Sotelo-Fonseca
    given-names: Jesus Emiliano
  - family-names: Alquicira-Hernandez
    given-names: Jose
  - family-names: Salgado
    given-names: Heladia
  - family-names: Collado-Torres
    given-names: Leonardo
    email: lcolladotor@gmail.com
    orcid: https://orcid.org/0000-0003-2140-308X
  - family-names: Reyes
    given-names: Alejandro
    email: alejandro.reyes.ds@gmail.com
    orcid: https://orcid.org/0000-0001-8717-6612
  year: '2024'
  url: http://www.bioconductor.org/packages/regutools
  notes: https://github.com/comunidadbioinfo/regutools - R package version 1.17.0
  doi: 10.18129/B9.bioc.regutools
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ComunidadBioInfo/regutools
url: https://support.bioconductor.org/t/regutools
date-released: '2021-11-15'
contact:
- family-names: Chavez
  given-names: Joselyn
  email: joselynchavezf@gmail.com
  orcid: https://orcid.org/0000-0002-4974-4591
references:
- type: article
  title: Programmatic access to bacterial regulatory networks with regutools
  authors:
  - family-names: Chávez
    given-names: Joselyn
  - family-names: Barberena-Jonas
    given-names: Carmina
  - family-names: Sotelo-Fonseca
    given-names: Jesus Emiliano
  - family-names: Alquicira-Hernandez
    given-names: Jose
  - family-names: Salgado
    given-names: Heladia
  - family-names: Collado-Torres
    given-names: Leonardo
  - family-names: Reyes
    given-names: Alejandro
  year: '2020'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/btaa575
  url: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa575/5861528