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# derfinder
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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
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
print(citation("derfinder"), bibtex = TRUE)
#> To cite package 'derfinder' in publications use:
#>
#> Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B,
#> Irizarry RA, Leek JT, Jaffe AE (2017). "Flexible expressed region
#> analysis for RNA-seq with derfinder." _Nucl. Acids Res._.
#> doi:10.1093/nar/gkw852 <https://doi.org/10.1093/nar/gkw852>,
#> <http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Flexible expressed region analysis for RNA-seq with derfinder},
#> author = {Leonardo Collado-Torres and Abhinav Nellore and Alyssa C. Frazee and Christopher Wilks and Michael I. Love and Ben Langmead and Rafael A. Irizarry and Jeffrey T. Leek and Andrew E. Jaffe},
#> year = {2017},
#> journal = {Nucl. Acids Res.},
#> doi = {10.1093/nar/gkw852},
#> url = {http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852},
#> }
#>
#> Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT (2014).
#> "Differential expression analysis of RNA-seq data at single-base
#> resolution." _Biostatistics_, *15 (3)*, 413-426.
#> doi:10.1093/biostatistics/kxt053
#> <https://doi.org/10.1093/biostatistics/kxt053>,
#> <http://biostatistics.oxfordjournals.org/content/15/3/413.long>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Differential expression analysis of RNA-seq data at single-base resolution},
#> author = {Alyssa C. Frazee and Sarven Sabunciyan and Kasper D. Hansen and Rafael A. Irizarry and Jeffrey T. Leek},
#> year = {2014},
#> journal = {Biostatistics},
#> volume = {15 (3)},
#> pages = {413-426},
#> doi = {10.1093/biostatistics/kxt053},
#> url = {http://biostatistics.oxfordjournals.org/content/15/3/413.long},
#> }
#>
#> Collado-Torres L, Jaffe AE, Leek JT (2017). _derfinder:
#> Annotation-agnostic differential expression analysis of RNA-seq data
#> at base-pair resolution via the DER Finder approach_.
#> doi:10.18129/B9.bioc.derfinder
#> <https://doi.org/10.18129/B9.bioc.derfinder>,
#> https://github.com/lcolladotor/derfinder - R package version 1.35.0,
#> <http://www.bioconductor.org/packages/derfinder>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach},
#> author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#> year = {2017},
#> url = {http://www.bioconductor.org/packages/derfinder},
#> note = {https://github.com/lcolladotor/derfinder - R package version 1.35.0},
#> doi = {10.18129/B9.bioc.derfinder},
#> }
```
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 *[usethis](https://CRAN.R-project.org/package=usethis)*,
*[remotes](https://CRAN.R-project.org/package=remotes)*,
*[sysreqs](https://github.com/r-hub/sysreqs)* and
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized
to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
*[BiocCheck](https://bioconductor.org/packages/3.17/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
- The [documentation website](http://lcolladotor.github.io/derfinder) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
This package was developed using
*[biocthis](https://bioconductor.org/packages/3.17/biocthis)*.
