regutools
regutools: an R package for data extraction from RegulonDB
Bioconductor version: 3.23 · Package version: 1.24.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("regutools")Details
| Maintainer | Joselyn Chavez <joselynchavezf@gmail.com> |
| Author | Joselyn Chavez [aut, cre] (ORCID: <https://orcid.org/0000-0002-4974-4591>), Carmina Barberena-Jonas [aut] (ORCID: <https://orcid.org/0000-0001-7413-638X>), Jesus E. Sotelo-Fonseca [aut] (ORCID: <https://orcid.org/0000-0003-1600-2396>), Jose Alquicira-Hernandez [ctb] (ORCID: <https://orcid.org/0000-0002-9049-7780>), Heladia Salgado [ctb] (ORCID: <https://orcid.org/0000-0002-3166-5801>), Leonardo Collado-Torres [aut] (ORCID: <https://orcid.org/0000-0003-2140-308X>), Alejandro Reyes [aut] (ORCID: <https://orcid.org/0000-0001-8717-6612>) |
| License | Artistic-2.0 |
| URL | https://github.com/ComunidadBioInfo/regutools |
| Bug Reports | https://support.bioconductor.org/t/regutools |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneRegulation, Network, NetworkInference, Software, SystemsBiology, Transcription, Visualization |
| Package Short Url | https://bioconductor.org/packages/regutools/ |
Citation
From within R, enter citation("regutools"):
Joselyn Chavez, Carmina Barberena-Jonas, Jesus E. Sotelo-Fonseca, Leonardo Collado-Torres, Alejandro Reyes. regutools: regutools: an R package for data extraction from RegulonDB. doi:10.18129/B9.bioc.regutools, R package version 1.24.0, https://bioconductor.org/packages/regutools.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | regutools_1.24.0.tar.gz |
| Windows binary (x86_64) | regutools_1.24.0.zip |
| macOS binary (arm64) | regutools_1.24.0.tgz |
| macOS binary (x86_64) | regutools_1.24.0.tgz |
Dependencies
Depends: R (>= 4.0)
Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache
Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr