regutools

The "regutools" R package for programmatic access to RegulonDB data is a valuable resource for transcriptional regulation in Escherichia coli K12. By providing a bridge between RegulonDB data and the Bioconductor ecosystem, regutools enables researchers to create reproducible workflows with automated queries to RegulonDB. The package integrates seamlessly with Bioconductor, utilizing its data structures and statistical methods.

Topic

Transcription factors and regulatory sites;Molecular interactions, pathways and networks;Gene regulation;Gene structure

Detail

  • Operation: Data retrieval;DNA transcription;Gene regulatory network analysis

  • Software interface: Command-line user interface

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.14.0

  • Credit: UNAM, NIH, CONACyT México scholarship.

  • Input: -

  • Output: -

  • Contact: Joselyn Chavez joselynchavezf@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Programmatic access to bacterial regulatory networks with regutools
  • Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernández J, Salgado H, Collado-Torres L, Reyes A. Programmatic access to bacterial regulatory networks with regutools. Bioinformatics. 2020 Aug 15;36(16):4532-4534. doi: 10.1093/bioinformatics/btaa575. PMID: 32573705; PMCID: PMC7575047.
  • https://doi.org/10.1093/bioinformatics/btaa575
  • PMID: 32573705
  • PMC: PMC7575047

Download and documentation

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