To cite R/qtl in publications use:

Broman KW, Wu H, Sen Ś, Churchill GA (2003). “R/qtl: QTL mapping in experimental crosses.” Bioinformatics, 19, 889-890. doi:10.1093/bioinformatics/btg112, https://academic.oup.com/bioinformatics/article-pdf/19/7/889/499910/btg112.pdf, https://doi.org/10.1093/bioinformatics/btg112.

Corresponding BibTeX entry:

  @Article{Broman2003,
    title = {R/qtl: {QTL} mapping in experimental crosses},
    author = {Karl W. Broman and Hao Wu and Śaunak Sen and Gary A.
      Churchill},
    journal = {Bioinformatics},
    year = {2003},
    volume = {19},
    pages = {889-890},
    doi = {10.1093/bioinformatics/btg112},
    url = {https://doi.org/10.1093/bioinformatics/btg112},
    eprint =
      {https://academic.oup.com/bioinformatics/article-pdf/19/7/889/499910/btg112.pdf},
  }