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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # regutools <img src="man/figures/logo.png" align="right" width="150px"/> <!-- badges: start --> [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) [![BioC status](http://www.bioconductor.org/shields/build/release/bioc/regutools.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/regutools) [![BioC dev status](http://www.bioconductor.org/shields/build/devel/bioc/regutools.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/regutools) [![Codecov test coverage](https://codecov.io/gh/ComunidadBioInfo/regutools/branch/master/graph/badge.svg)](https://codecov.io/gh/ComunidadBioInfo/regutools?branch=master) [![R build status](https://github.com/ComunidadBioInfo/regutools/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/ComunidadBioInfo/regutools/actions) [![Support site activity, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.](http://www.bioconductor.org/shields/posts/regutools.svg)](https://support.bioconductor.org/t/regutools/) [![GitHub issues](https://img.shields.io/github/issues/comunidadbioinfo/regutools)](https://github.com/comunidadbioinfo/regutools/issues) <!-- badges: end --> The goal of `regutools` is to provide an R interface for extracting and processing data from [RegulonDB](http://regulondb.ccg.unam.mx/). This package was created as a collaboration by members of the [Community of Bioinformatics Software Developers](https://comunidadbioinfo.github.io/) (CDSB in Spanish). For more details, please check the [documentation website](http://comunidadbioinfo.github.io/regutools) or the Bioconductor package landing page [here](https://bioconductor.org/packages/regutools). ## Installation You can install the released version of `regutools` from [Bioconductor](http://bioconductor.org/) with: ``` r 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](https://github.com/) with: ``` r BiocManager::install("ComunidadBioinfo/regutools") ``` ## Example This is a basic example which shows you how to use `regutools`. For more details, please check the vignette. ``` r 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](http://bioconductor.org/packages/regutools) or at the [documentation website](http://comunidadbioinfo.github.io/regutools). ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `regutools` from [Bioconductor](http://bioconductor.org/) using the following code: ``` r 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**. ``` r 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](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms. ## Development tools - Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, *[sysreqs](https://github.com/r-hub/sysreqs)* and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.14/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://comunidadbioinfo.github.io/regutools) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The code is styled automatically thanks to *[styler](https://CRAN.R-project.org/package=styler)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. For more details, check the `dev` directory. This package was developed using *[biocthis](https://bioconductor.org/packages/3.14/biocthis)*. # RegulonDB <a href="http://regulondb.ccg.unam.mx/"><img src="http://regulondb.ccg.unam.mx/img/logo.jpg"></a> # A CDSB community project <a href="https://comunidadbioinfo.github.io/"><img src="https://comunidadbioinfo.github.io/img/Logo_texto-768x107.png"></a>