derfinder

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.

Documentation

For more information about derfinder check the vignettes through Bioconductor or at the documentation website.

Further documentation

You can generate HTML reports from the results using regionReport available here.

Installation instructions

Get the latest stable R release from CRAN. Then install derfinder from Bioconductor using the following code:

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.

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.
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. 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. By contributing to this project, you agree to abide by its terms.

Development tools

Continuous code testing is possible thanks to GitHub actions through usethis, remotes, sysreqs and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The code is styled automatically thanks to styler.
The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.