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 (3.24)
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]
, Carmina Barberena-Jonas [aut]
, Jesus E. Sotelo-Fonseca [aut]
, Jose Alquicira-Hernandez [ctb]
, Heladia Salgado [ctb]
, Leonardo Collado-Torres [aut]
, Alejandro Reyes [aut]
Maintainer: Joselyn Chavez <joselynchavezf at gmail.com>
citation("regutools")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneRegulation, Network, NetworkInference, Software, SystemsBiology, Transcription, Visualization |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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 |
See More
| 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_1.25.0.tar.gz |
| Windows Binary (x86_64) | regutools_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | regutools_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | regutools_1.25.0.tgz |
| 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 |