To cite R/ctl in publications use:

Arends D, Li Y, Brockmann G, Jansen R, Williams R, Prins P (2016). “Correlation Trait Loci CTL mapping: phenotype network inference subject to genotype.” Journal of Open Source Software, 1, 87-87. doi: 10.21105/joss.00087.

Corresponding BibTeX entry:

  @Article{,
    title = {Correlation Trait Loci {CTL} mapping: phenotype network
      inference subject to genotype},
    author = {Danny Arends and Yang Li and Gudrun A. Brockmann and
      Ritsert C. Jansen and Robert W. Williams and Pjotr Prins},
    journal = {Journal of Open Source Software},
    year = {2016},
    volume = {1},
    issue = {6},
    pages = {87-87},
    doi = {10.21105/joss.00087},
  }