This is the development version of regutools; for the stable release version, see regutools.
regutools: an R package for data extraction from RegulonDBBioconductor version: Development (3.22)
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.
Author: Joselyn Chavez [aut, cre] ORCID: 0000-0002-4974-4591 , Carmina Barberena-Jonas [aut] ORCID: 0000-0001-7413-638X , Jesus E. Sotelo-Fonseca [aut] ORCID: 0000-0003-1600-2396 , Jose Alquicira-Hernandez [ctb] ORCID: 0000-0002-9049-7780 , Heladia Salgado [ctb] ORCID: 0000-0002-3166-5801 , Leonardo Collado-Torres [aut] ORCID: 0000-0003-2140-308X , Alejandro Reyes [aut] ORCID: 0000-0001-8717-6612
Maintainer: Joselyn Chavez <joselynchavezf at gmail.com>
Citation (from within R, entercitation("regutools")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("regutools")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("regutools")Follow Installation instructions to use this package in your R session.
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