output: github_document

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# regutools <img src="man/figures/logo.png" align="right" width="150px"/> 

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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)) {


## Check that you have a valid Bioconductor installation

And the development version from [GitHub](https://github.com/) with:

```{r 'install devel', eval = FALSE}

## Example

This is a basic example which shows you how to use `regutools`. For more details, please check the vignette.

```{r example}
## 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 <-
        database_conn = regulondb_conn,
        organism = "E.coli",
        database_version = "1",
        genome_version = "1"

## Get the araC regulators
araC_regulation <-
        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)) {


## 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>