To cite DECIPHER in publications use:

  Wright ES (2016). “Using DECIPHER v2.0 to Analyze Big Biological
  Sequence Data in R.” _The R Journal_, *8*(1), 352-359.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R},
    author = {Erik S. Wright},
    journal = {The R Journal},
    year = {2016},
    volume = {8},
    number = {1},
    pages = {352-359},
  }

To cite individual functions within DECIPHER, please refer to the
reference section in the function's manual (help) page where available.