title: destiny: diffusion maps for large-scale single-cell data in R.
abstract: : 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.
  
  
  
  destiny is an open-source R/Bioconductor package "bioconductor.org/packages/destiny" also available at www.helmholtz-muenchen.de/icb/destiny A detailed vignette describing functions and workflows is provided with the package.
  
  
  
  carsten.marr@helmholtz-muenchen.de or f.buettner@helmholtz-muenchen.de
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and.
authors.forename: Philipp
authors.initials: P
authors.lastname: Angerer
authors.affiliation: Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and.
authors.forename: Laleh
authors.initials: L
authors.lastname: Haghverdi
authors.affiliation: Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and.
authors.forename: Maren
authors.initials: M
authors.lastname: Büttner
authors.affiliation: Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Boltzmannstr. 3, 85748 Garching, Germany.
authors.forename: Fabian J
authors.initials: FJ
authors.lastname: Theis
authors.affiliation: Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and.
authors.forename: Carsten
authors.initials: C
authors.lastname: Marr
authors.affiliation: Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and.
authors.forename: Florian
authors.initials: F
authors.lastname: Buettner
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D004058:Diffusion; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software