To cite the 'triplex' package in publications use:

  Hon J, Martinek T, Rajdl K, Lexa M. Triplex: an R/Bioconductor
  package for identification and visualization of potential
  intramolecular triplex patterns in DNA sequences. Bioinformatics.
  2013 Aug 1;29(15):1900-1. doi: 10.1093/bioinformatics/btt299.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences},
    author = {Jiri Hon and Tomas Martinek and Kamil Rajdl and Matej Lexa},
    year = {2013},
    doi = {10.1093/bioinformatics/btt299},
    url = {http://bioinformatics.oxfordjournals.org/content/early/2013/05/24/bioinformatics.btt299.abstract},
    eprint = {http://bioinformatics.oxfordjournals.org/content/early/2013/05/24/bioinformatics.btt299.full.pdf+html},
    journal = {Bioinformatics},
  }