To cite DMCHMM in publications use:

  Farhad Shokoohi (2020) DMCHMM: an R package to identify
  differentially methylated CpG Sites using Hidden Markov Models,
  Version 1.11.1, DOI: 10.18129/B9.bioc.DMCHMMURL
  http://bioconductor.org/packages/DMCHMM/

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {DMCHMM: an R package to identify differentially
         methylated CpG Sites using Hidden Markov Models, Version 1.11.1,
         DOI: 10.18129/B9.bioc.DMCHMM},
    author = {Farhad Shokoohi},
    year = {2020},
    url = {http://bioconductor.org/packages/DMCHMM/},
  }

  Shokoohi F., Stephens D., Bourque G., Pastinen T., Greenwood C. and
  Labbe A. (2018). A Hidden Markov Model for Identifying Differentially
  Methylated Sites in Bisulfite Sequencing Data. Biometrics. 75 210-221
  DOI: 10.1111/biom.12965

A BibTeX entry for LaTeX users is

  @Article{,
    title = {A Hidden Markov Model for Identifying Differentially
    Methylated Sites in Bisulfite Sequencing Data},
    author = {Farhad Shokoohi and David Stephens and Guillaume Bourque and Tomi Pastinen and Celia Greenwood and Aurelie Labbe},
    year = {2018},
    journal = {Biometrics},
    volume = {75},
    page = {210--221},
    url = {https://doi.org/10.1111/biom.12965},
  }