destiny: diffusion maps for large scale single cell data in R
UNLABELLED 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.
Bioinform.