destiny: diffusion maps for large-scale single-cell data in R


  • P. Angerer
  • L. Haghverdi
  • M. Büttner
  • F.J. Theis
  • C. Marr
  • F. Buettner


  • Bioinformatics


  • Bioinformatics 32 (8): 1241-1243


  • SUMMARY: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single-cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming. AVAILABILITY AND IMPLEMENTATION: destiny is an open-source R/Bioconductor package “” also available at A detailed vignette describing functions and workflows is provided with the package.