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. 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. 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://github.com/lcolladotor/derfinder - R package version 1.47.0, http://www.bioconductor.org/packages/derfinder.

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }

  @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 1.47.0},
    doi = {10.18129/B9.bioc.derfinder},
  }