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Destiny: Diffusion maps for large-scale single-cell data in R.

Bioinformatics 32, 1241-1243 (2016)
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Open Access Green
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 http://bioconductor.org/packages/destiny also available at https://www.helmholtz-muenchen.de/icb/destiny. A detailed vignette describing functions and workflows is provided with the package.
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Publication type Article: Journal article
Document type Scientific Article
ISSN (print) / ISBN 1367-4803
Journal Bioinformatics
Quellenangaben Volume: 32, Issue: 8, Pages: 1241-1243 Article Number: , Supplement: ,
Publisher Oxford University Press
Publishing Place Oxford
Reviewing status Peer reviewed