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This is the development version of destiny; for the stable release version, see destiny.

Creates diffusion maps

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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 3.19.0
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, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d
System Requirements C++11
Bug Reports
See More
Suggests knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq,, scran, repr
Linking To Rcpp, RcppEigen, grDevices
Enhances rgl, SingleCellExperiment
Depends On Me
Imports Me
Suggests Me CelliD, CellTrails, monocle
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package destiny_3.19.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) destiny_3.19.0.tgz
macOS Binary (arm64) destiny_3.19.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats