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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, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/"
)
```
# GenomicState
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#stable)
[](http://bioconductor.org/packages/stats/data-annotation/GenomicState)
[](https://support.bioconductor.org/tag/GenomicState)
[](https://codecov.io/gh/LieberInstitute/GenomicState?branch=devel)
[](https://github.com/LieberInstitute/GenomicState/actions/workflows/check-bioc.yml)
[](https://github.com/LieberInstitute/GenomicState/issues)
[](https://github.com/LieberInstitute/GenomicState/pulls)
<!-- badges: end -->
This package provides functions for building `GenomicState` objects from diverse annotation sources such as [`Gencode`](https://www.gencodegenes.org/human/releases.html). It also provides a way to load pre-computed `GenomicState` objects if you are working at [JHPCE](https://jhpce.jhu.edu/). These `GenomicState` objects are normally created using [derfinder::makeGenomicState()](http://lcolladotor.github.io/derfinder/reference/makeGenomicState.html) and can be used for annotating regions with [derfinder::annotateRegions()](http://lcolladotor.github.io/derfinder/reference/annotateRegions.html) which are in turn used by [derfinderPlot::plotRegionCoverage()](http://leekgroup.github.io/derfinderPlot/reference/plotRegionCoverage.html).
## Documentation
For more information about `GenomicState` check the vignettes [through Bioconductor](http://bioconductor.org/packages/GenomicState) or at the [documentation website](http://lieberinstitute.github.io/GenomicState).
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `GenomicState` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("GenomicState")
```
## Citation
Below is the citation output from using `citation('GenomicState')` in R. Please
run this yourself to check for any updates on how to cite __GenomicState__.
```{r 'citation', eval = requireNamespace('GenomicState')}
print(citation("GenomicState"), bibtex = TRUE)
```
Please note that the `GenomicState` 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://lieberinstitute.github.io/GenomicState) 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')`.