regutools

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.

Installation

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")

Example

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(): 2021-08-03
#> 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

Documentation

For more information about regutools check the vignettes through Bioconductor or at the documentation website.

Installation instructions

Get the latest stable R release from CRAN. Then install regutools from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
  }

BiocManager::install("regutools")

Citation

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 (2021). _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
#> 1.5.0, <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 = {2021},
#>     url = {http://www.bioconductor.org/packages/regutools},
#>     note = {https://github.com/comunidadbioinfo/regutools - R package version 1.5.0},
#>     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.

Code of Conduct

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.

Development tools

Continuous code testing is possible thanks to GitHub actions through usethis, remotes, sysreqs and rcmdcheck customized to use Bioconductor's docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The code is styled automatically thanks to styler.
The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.

ComunidadBioInfo/regutools