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

doi:10.1093/bioinformatics/btv715

. 2016 Apr 15;32(8):1241-3.

doi: 10.1093/bioinformatics/btv715. Epub 2015 Dec 14.

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

Philipp Angerer¹, Laleh Haghverdi¹, Maren Büttner¹, Fabian J Theis², Carsten Marr¹, Florian Buettner¹

Affiliations

¹ Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and.
² 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.

PMID: 26668002
DOI: 10.1093/bioinformatics/btv715

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

Philipp Angerer et al. Bioinformatics. 2016.

. 2016 Apr 15;32(8):1241-3.

doi: 10.1093/bioinformatics/btv715. Epub 2015 Dec 14.

Authors

Philipp Angerer¹, Laleh Haghverdi¹, Maren Büttner¹, Fabian J Theis², Carsten Marr¹, Florian Buettner¹

Affiliations

¹ Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and.
² 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.

PMID: 26668002
DOI: 10.1093/bioinformatics/btv715

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.

Availability and implementation: 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.

Contact: carsten.marr@helmholtz-muenchen.de or f.buettner@helmholtz-muenchen.de

Supplementary information: Supplementary data are available at Bioinformatics online.

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

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

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