To cite package ‘crupR’ in publications use:

  Ramisch, A., Heinrich, V., Glaser, L.V. et al. CRUP: a comprehensive
  framework to predict condition-specific regulatory units. Genome Biol
  20, 227 (2019). https://doi.org/10.1186/s13059-019-1860-7

A BibTeX entry for LaTeX users is

  @Article{,
    title = {CRUP: a comprehensive framework to predict condition-specific regulatory units},
    author = {Verena Heinrich and Anna Ramisch and Martin Vingron},
    year = {2019},
    journal = {Genome Biology},
    doi = {10.1186/s13059-019-1860-7},
    volume = {20},
    issue = {1},
    pages = {227},
  }