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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%"
)
```
# MyBioconductorPackage
<!-- badges: start -->
[](https://github.com/kevinrue/MyBioconductorPackage/issues)
[](https://github.com/kevinrue/MyBioconductorPackage/pulls)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://github.com/kevinrue/MyBioconductorPackage/actions)
[](https://app.codecov.io/gh/kevinrue/MyBioconductorPackage?branch=main)
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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.