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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%"
)
```
# derfinder
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/derfinder)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder)
[](http://bioconductor.org/packages/stats/bioc/derfinder/)
[](https://support.bioconductor.org/tag/derfinder)
[](https://bioconductor.org/packages/release/bioc/html/derfinder.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder/)
[](https://bioconductor.org/packages/release/bioc/html/derfinder.html#since)
[](https://codecov.io/gh/lcolladotor/derfinder?branch=devel)
[](https://github.com/lcolladotor/derfinder/actions/workflows/check-bioc.yml)
[](https://github.com/lcolladotor/derfinder/issues)
[](https://github.com/lcolladotor/derfinder/pulls)
<!-- badges: end -->
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach. This package contains two different implementations of this approach. The first one is the single base-level F-statistics implementation and the second one is via identifying expressed regions. For more information about `derfinder` check the vignettes [here](http://www.bioconductor.org/packages/derfinder).
## Documentation
For more information about `derfinder` check the vignettes [through Bioconductor](http://bioconductor.org/packages/derfinder) or at the [documentation website](http://lcolladotor.github.io/derfinder).
## Further documentation
You can generate HTML reports from the results using __regionReport__
available [here](https://github.com/lcolladotor/regionReport).
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `derfinder` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("derfinder")
```
## Citation
Below is the citation output from using `citation('derfinder')` in R. Please
run this yourself to check for any updates on how to cite __derfinder__.
```{r 'citation', eval = requireNamespace('derfinder')}
print(citation("derfinder"), bibtex = TRUE)
```
Please note that the `derfinder` 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.
## DER Finder versions
* The original implementation of the DER Finder approach as published in Frazee et al, Biostatistics 2014 is available via GitHub at [derfinder](https://github.com/leekgroup/derfinder).
* The version implementing the single base-level approach via calculating F-stastics as described in the pre-print Collado-Torres et al, Nucleic Acids Research 2017 is available via Bioconductor at [derfinder](http://bioconductor.org/packages/derfinder). The same package has the functions required for the expressed regions-level approach.
## Code of Conduct
Please note that the derfinder 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://lcolladotor.github.io/derfinder) 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')`.