To cite package ‘methylPipe’ in publications use:

  Kamal Kishore et al. (2015): methylPipe and compEpiTools: a suite of
  R packages for the integrative analysis of epigenomics data. BMC
  Bioinformatics

A BibTeX entry for LaTeX users is

  @Article{,
    title = {methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.},
    author = {Kamal Kishore and Stefano {de Pretis} and Ryan Lister and Marco J Morelli and Valerio Bianchi and Bruno Amati and Joseph R. Ecker and Mattia Pelizzola},
    year = {2015},
    journal = {BMC Bioinformatics},
    doi = {10.1186/s12859-015-0742-6},
  }