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 1.18.9, http://www.bioconductor.org/packages/derfinder.