destiny

Destiny is an R package that provides an efficient implementation of the diffusion map algorithm, which is a spectral method for non-linear dimension reduction. It has been adapted for the visualization of single-cell expression data and includes a single-cell specific noise model allowing for missing and censored values. Destiny further presents an efficient nearest-neighbor approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. The package has been exemplarily applied to a recent time-resolved mass cytometry dataset of cellular reprogramming.

Topic

Data mining;Data visualisation;Embryology

Detail

  • Operation: Data handling;Multiple sample visualisation;Gene expression comparison

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License, version 3

  • Cost: Free

  • Version name: 3.12.0

  • Credit: UK Medical Research Council, the Bavarian Research Network for Molecular Biosystems (BioSysNet), the ERC , DFG Fellowship through the Graduate School of Quantitative Biosciences Munich (QBM).

  • Input: -

  • Output: -

  • Contact: Philipp Angerer philipp.angerer@helmholtz-muenchen.de

  • Collection: -

  • Maturity: Mature

Publications

  • destiny: diffusion maps for large-scale single-cell data in R.
  • Angerer P, et al. destiny: diffusion maps for large-scale single-cell data in R. destiny: diffusion maps for large-scale single-cell data in R. 2016; 32:1241-3. doi: 10.1093/bioinformatics/btv715
  • https://doi.org/10.1093/bioinformatics/btv715
  • PMID: 26668002
  • PMC: -

Download and documentation

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