To cite DECIPHER in publications use:

  Wright ES (2024). “Fast and Flexible Search for Homologous Biological
  Sequences with DECIPHER v3.” _The R Journal_, *16*(2), 191-200.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Fast and Flexible Search for Homologous Biological Sequences with DECIPHER v3},
    author = {Erik S. Wright},
    journal = {The R Journal},
    year = {2024},
    volume = {16},
    number = {2},
    pages = {191-200},
  }

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