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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%"
)
```
# ScreenR <a href='https://emanuelsoda.github.io/ScreenR/'><img src='man/figures/logo.png' align="right" height="120" /></a>
<!-- badges: start -->
[](https://codecov.io/gh/EmanuelSoda/ScreenR) [](https://github.com/EmanuelSoda/ScreenR/issues) [](https://github.com/EmanuelSoda/ScreenR/pulls) [](https://github.com/EmanuelSoda/ScreenR/network/members) []() []() []() []()
[](https://github.com/EmanuelSoda/ScreenR/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
ScreenR is an easy and effective package to perform hits identification in loss of function High Throughput Biological Screening performed with shRNAs library. ScreenR combines the power of software like edgeR with the simplicity of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts data and integrates a wide range of visualization for each step of the analysis
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/) note
that you need to have `R 4.3` or greater to use `ScreenR`. Then install
`ScreenR` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("ScreenR")
```
And the development version from [GitHub](https://github.com/EmanuelSoda/ScreenR) with:
```{r 'install_dev', eval = FALSE}
devtools::install_github("EmanuelSoda/ScreenR")
```
## ScreenR overall workflow
<img src="man/figures/Pipeline.png" align="top">
Please note that the `ScreenR` 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.
## Citation
Below is the citation output from using `citation('ScreenR')` in `R`. Please run this yourself to check for any updates on how to cite **ScreenR**.
```{r 'citation', eval = requireNamespace('ScreenR')}
print(citation('ScreenR'))
```
## Code of Conduct
Please note that the `ScreenR` 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://EmanuelSoda.github.io/ScreenR) 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')`.