To cite cloneRate in publications use:

  Johnson, B., Shuai, Y., Schweinsberg, J., Curtius, K. cloneRate: fast
  estimation of single-cell clonal dynamics using coalescent theory.
  Bioinformatics, 2023.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory},
    author = {Brian Johnson and Yubo Shuai and Jason Schweinsberg and Kit Curtius},
    journal = {Bioinformatics},
    year = {2023},
    url = {https://doi.org/10.1093/bioinformatics/btad561},
  }