To cite package ‘destiny’ in publications use:

  Philipp Angerer et al. (2015): destiny: diffusion maps for
  large-scale single-cell data in R. Helmholtz-Zentrum München. URL:
  <http://bioinformatics.oxfordjournals.org/content/32/8/1241>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {destiny: diffusion maps for large-scale single-cell data in R},
    volume = {32},
    number = {8},
    url = {http://bioinformatics.oxfordjournals.org/content/32/8/1241},
    doi = {10.1093/bioinformatics/btv715},
    journal = {Bioinformatics},
    author = {Philipp Angerer and Laleh Haghverdi and Maren Büttner and Fabian Theis and Carsten Marr and Florian Büttner},
    pages = {1241 1242 1243},
    organization = {Helmholtz-Zentrum München},
    address = {Ingolstädter Landstraße 1, Neuherberg, Germany},
    year = {2015},
    note = {More information at <http://www.helmholtz-muenchen.de/icb/destiny>},
  }