Collado-Torres L, Frazee AC, Jaffe AE and Leek JT (2014). derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution. https://github.com/lcolladotor/derfinder - R package version 1.0.10, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html.

Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA and Leek JT (2014). “Differential expression analysis of RNA-seq data at single-base resolution.” Biostatistics, 15 (3), pp. 413-426. http://dx.doi.org/10.1093/biostatistics/kxt053, http://biostatistics.oxfordjournals.org/content/15/3/413.long.