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 1.39.0,
  <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 1.39.0},
    doi = {10.18129/B9.bioc.derfinder},
  }