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Creates diffusion maps

Bioconductor version: Release (3.18)

Create and plot diffusion maps.

Author: Philipp Angerer [cre, aut] , Laleh Haghverdi [ctb], Maren Büttner [ctb] , Fabian Theis [ctb] , Carsten Marr [ctb] , Florian Büttner [ctb]

Maintainer: Philipp Angerer <phil.angerer at gmail.com>

Citation (from within R, enter citation("destiny")):


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To view documentation for the version of this package installed in your system, start R and enter:

destiny 2.0 brought the Diffusion Pseudo Time (DPT) class HTML R Script
destiny main vignette: Start here! HTML R Script
detecting relevant genes with destiny 3 HTML R Script
Reproduce the Diffusion Map vignette with the supplied data() HTML R Script
The effects of a global vs. local kernel HTML R Script
tidyverse and ggplot integration with destiny HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, CellBiology, Clustering, Software, Visualization
Version 3.16.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.4.0)
Imports methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d
System Requirements C++11
URL https://theislab.github.io/destiny/ https://github.com/theislab/destiny/ https://www.helmholtz-muenchen.de/icb/destiny https://bioconductor.org/packages/destiny https://doi.org/10.1093/bioinformatics/btv715
Bug Reports https://github.com/theislab/destiny/issues
See More
Suggests knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr
Linking To Rcpp, RcppEigen, grDevices
Enhances rgl, SingleCellExperiment
Depends On Me
Imports Me phemd
Suggests Me CelliD, CellTrails, monocle
Links To Me
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Source Package destiny_3.16.0.tar.gz
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