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>.

Corresponding BibTeX entry:

  @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},
  }