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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%"
)
```
# BSA
<!-- badges: start -->
[](https://github.com/cmatKhan/BSA/issues)
[](https://github.com/cmatKhan/BSA/pulls)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://github.com/cmatKhan/BSA/actions/workflows/check-bioc.yml)
[](https://app.codecov.io/gh/cmatKhan/BSA?branch=master)
[](https://zenodo.org/badge/latestdoi/520266986)
<!-- badges: end -->
The goal of `BSA` is to reimplement Daniel's BSA2 code in a package structure
such that it may be installed using R `install`. This may also form the seed
of either a software or
[workflow](https://contributions.bioconductor.org/non-software.html) package on bioconductor.
## Installation
```{r 'install -- real', eval = FALSE}
install.packages("remotes")
remotes::install_github("cmatKhan/BSA")
```
## Usage
The first thing that you will need to do iscreate a samplesheet and process
the data through the [BSA processing pipeline](https://github.com/cmatKhan/variant_calling_and_bsa).
Instructions for creating this samplesheet are in the Article (above) called
`CreatePipelineSampleSheet`.
Next, you will be using the functions in this package to analyze the data. An
example of the process are in `BSA3` and `BSA6`.
## Citation
Below is the citation output from using `citation('BSA')` in R. Please
run this yourself to check for any updates on how to cite __BSA__.
```{r 'citation', eval = requireNamespace('BSA')}
print(citation('BSA'), bibtex = TRUE)
```
Please note that the `BSA` 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 `BSA` 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://cmatKhan.github.io/BSA) 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')`.