Introduction

: 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.deSupplementary data are available at Bioinformatics online.

Publications

  1. destiny: diffusion maps for large-scale single-cell data in R.
    Cite this
    Angerer P, Haghverdi L, Büttner M, Theis FJ, Marr C, Buettner F, 2016-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Philipp Angerer
    Developer

    Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Germany

  2. Laleh Haghverdi
    Developer

    Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Germany

  3. Maren Büttner
    Developer

    Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Germany

  4. Fabian J Theis
    Developer

    Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Germany

  5. Carsten Marr
    Developer

    Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Germany

  6. Florian Buettner
    Investigator

    Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Germany

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Summary
AccessionBT000215
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByFlorian Buettner