Please cite the paper below when using casper, and the appropriate methodology articles indicated in the help page of the functions you're using.

Rossell D, Stephan-Otto Attolini C, Kroiss M, Stocker A (2014). “Quantifying alternative splicing from paired-end RNA-seq data.” Annals of Applied Statistics, 8(1), 309–330.

Corresponding BibTeX entry:

  @Article{,
    author = {D. Rossell and C. {Stephan-Otto Attolini} and M. Kroiss
      and A. Stocker},
    title = {Quantifying alternative splicing from paired-end RNA-seq
      data},
    journal = {Annals of Applied Statistics},
    year = {2014},
    volume = {8},
    number = {1},
    pages = {309--330},
  }