The goal of regutools
is to provide an R interface for extracting and
processing data from RegulonDB. This
package was created as a collaboration by members of the Community of
Bioinformatics Software Developers
(CDSB in Spanish).
For more details, please check the documentation website or the Bioconductor package landing page here.
You can install the released version of regutools
from
Bioconductor with:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("regutools")
## Check that you have a valid Bioconductor installation
BiocManager::valid()
And the development version from GitHub with:
BiocManager::install("ComunidadBioinfo/regutools")
This is a basic example which shows you how to use regutools
. For more
details, please check the vignette.
library("regutools")
## basic example code
## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) regulondb_conn <- connect_database()
#> snapshotDate(): 2020-10-27
#> adding rname 'https://www.dropbox.com/s/ufp6wqcv5211v1w/regulondb_v10.8_sqlite.db?dl=1'
## Build a regulondb object
e_coli_regulondb <-
regulondb(
database_conn = regulondb_conn,
organism = "E.coli",
database_version = "1",
genome_version = "1"
)
## Get the araC regulators
araC_regulation <-
get_gene_regulators(
e_coli_regulondb,
genes = c("araC"),
format = "multirow",
output.type = "TF"
)
## Summarize the araC regulation
get_regulatory_summary(e_coli_regulondb, araC_regulation)
#> regulondb_result with 3 rows and 7 columns
#> TF Regulated_genes_per_TF Percent Activator Repressor
#> <character> <character> <character> <character> <character>
#> 1 AraC 1 33.3333333333333 0 0
#> 2 CRP 1 33.3333333333333 1 0
#> 3 XylR 1 33.3333333333333 0 1
#> Dual Regulated_genes
#> <character> <character>
#> 1 1 araC
#> 2 0 araC
#> 3 0 araC
For more information about regutools
check the vignettes through
Bioconductor or at the
documentation website.
Get the latest stable R
release from
CRAN. Then install regutools
using from
Bioconductor the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("regutools")
Below is the citation output from using citation('regutools')
in R.
Please run this yourself to check for any updates on how to cite
regutools.
print(citation("regutools"), bibtex = TRUE)
#>
#> Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernandez J,
#> Salgado H, Collado-Torres L, Reyes A (2020). _regutools: an R package
#> for data extraction from RegulonDB_. doi: 10.18129/B9.bioc.regutools
#> (URL: https://doi.org/10.18129/B9.bioc.regutools),
#> https://github.com/comunidadbioinfo/regutools - R package version
#> 1.3.3, <URL: http://www.bioconductor.org/packages/regutools>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {regutools: an R package for data extraction from RegulonDB},
#> author = {Joselyn Chávez and Carmina Barberena-Jonas and Jesus Emiliano Sotelo-Fonseca and Jose Alquicira-Hernandez and Heladia Salgado and Leonardo Collado-Torres and Alejandro Reyes},
#> year = {2020},
#> url = {http://www.bioconductor.org/packages/regutools},
#> note = {https://github.com/comunidadbioinfo/regutools - R package version 1.3.3},
#> doi = {10.18129/B9.bioc.regutools},
#> }
#>
#> Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernandez J,
#> Salgado H, Collado-Torres L, Reyes A (2020). "Programmatic access to
#> bacterial regulatory networks with regutools." _Bioinformatics_. doi:
#> 10.1093/bioinformatics/btaa575 (URL:
#> https://doi.org/10.1093/bioinformatics/btaa575), <URL:
#> https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa575/5861528>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Programmatic access to bacterial regulatory networks with regutools},
#> author = {Joselyn Chávez and Carmina Barberena-Jonas and Jesus Emiliano Sotelo-Fonseca and Jose Alquicira-Hernandez and Heladia Salgado and Leonardo Collado-Torres and Alejandro Reyes},
#> year = {2020},
#> journal = {Bioinformatics},
#> doi = {10.1093/bioinformatics/btaa575},
#> url = {https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa575/5861528},
#> }
Please note that the regutools
was only made possible thanks to many
other R and bioinformatics software authors, which are cited either in
the vignettes and/or the paper(s) describing this package.
Please note that the derfinderPlot project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
For more details, check the dev
directory.
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