To cite methylKit:

  Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E
  Garrett-Bakelman, Maria E Figueroa, Ari Melnick and Christopher E
  Mason. methylKit: a comprehensive R package for the analysis of
  genome-wide DNA methylation profiles. Genome Biology 13:R87 (2012).

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Altuna Akalin and Matthias Kormaksson and Sheng Li and Francine E. Garrett-Bakelman and Maria E. Figueroa and Ari Melnick and Christopher E Mason},
    title = {methylKit: a comprehensive R package for the
analysis of genome-wide DNA methylation profiles},
    journal = {Genome Biology},
    year = {2012},
    volume = {13},
    number = {10},
    pages = {R87},
  }

Thanks very much for using methylKit!, we appreciate if you remember to
cite it in your paper : ).