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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# regutools <img src="man/figures/logo.png" align="right" width="150px"/>
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/regutools)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/regutools)
[](https://codecov.io/gh/ComunidadBioInfo/regutools?branch=master)
[](https://github.com/ComunidadBioInfo/regutools/actions)
[](https://support.bioconductor.org/t/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 'install release', eval = FALSE}
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 'install devel', eval = FALSE}
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 example}
library("regutools")
## basic example code
## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) regulondb_conn <- connect_database()
## 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)
```
## 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 'install', eval = FALSE}
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 'citation', eval = requireNamespace('regutools')}
print(citation("regutools"), bibtex = TRUE)
```
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 `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, `r BiocStyle::Githubpkg('r-hub/sysreqs')` and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://comunidadbioinfo.github.io/regutools) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
This package was developed using `r BiocStyle::Biocpkg('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>