regutools

This is the development version of regutools; for the stable release version, see regutools.

regutools: an R package for data extraction from RegulonDB

Bioconductor version: Development (3.21)

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: ), Carmina Barberena-Jonas [aut] (ORCID: ), Jesus E. Sotelo-Fonseca [aut] (ORCID: ), Jose Alquicira-Hernandez [ctb] (ORCID: ), Heladia Salgado [ctb] (ORCID: ), Leonardo Collado-Torres [aut] (ORCID: ), Alejandro Reyes [aut] (ORCID: )

Maintainer: Joselyn Chavez <joselynchavezf at gmail.com>

Citation (from within R, enter citation("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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("regutools")

regutools: an R package for data extraction from RegulonDB	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneRegulation, Network, NetworkInference, Software, SystemsBiology, Transcription, Visualization
Version	1.19.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache
System Requirements
URL	https://github.com/ComunidadBioInfo/regutools
Bug Reports	https://support.bioconductor.org/t/regutools

Suggests	BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	regutools_1.19.0.tar.gz
Windows Binary (x86_64)	regutools_1.19.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/regutools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/regutools
Bioc Package Browser	https://code.bioconductor.org/browse/regutools/
Package Short Url	https://bioconductor.org/packages/regutools/
Package Downloads Report	Download Stats