README.Rmd

---
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%"
)
```

# MyBioconductorPackage

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The goal of `MyBioconductorPackage` is to ...

## Installation instructions

Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `MyBioconductorPackage` from [Bioconductor](http://bioconductor.org/) using the following code:

```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("MyBioconductorPackage")
```

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

```{r 'install_dev', eval = FALSE}
BiocManager::install("kevinrue/MyBioconductorPackage")
```

## Example

This is a basic example which shows you how to solve a common problem:

```{r example, eval = requireNamespace('MyBioconductorPackage')}
library("MyBioconductorPackage")
## basic example code
```

What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:

```{r cars}
summary(cars)
```

You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date.

You can also embed plots, for example:

```{r pressure, echo = FALSE}
plot(pressure)
```

In that case, don't forget to commit and push the resulting figure files, so they display on GitHub!

## Citation

Below is the citation output from using `citation('MyBioconductorPackage')` in R. Please
run this yourself to check for any updates on how to cite __MyBioconductorPackage__.

```{r 'citation', eval = requireNamespace('MyBioconductorPackage')}
print(citation('MyBioconductorPackage'), bibtex = TRUE)
```

Please note that the `MyBioconductorPackage` 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 `MyBioconductorPackage` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, 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://kevinrue.github.io/MyBioconductorPackage) 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')`.

## Code of Conduct

Please note that the MyBioconductorPackage project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.