destiny

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Creates diffusion maps

Bioconductor version: Development (3.24)

Create and plot diffusion maps.

Author: Philipp Angerer [cre, aut] ORCID: 0000-0002-0369-2888 , Laleh Haghverdi [ctb], Maren Büttner [ctb] ORCID: 0000-0002-6189-3792 , Fabian Theis [ctb] ORCID: 0000-0002-2419-1943 , Carsten Marr [ctb] ORCID: 0000-0003-2154-4552 , Florian Büttner [ctb] ORCID: 0000-0001-5587-6761

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

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

Philipp Angerer. destiny: Creates diffusion maps. doi:10.18129/B9.bioc.destiny, R package version 3.27.0, https://bioconductor.org/packages/destiny.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("destiny")

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

Documentation

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

browseVignettes("destiny")

Reproduce the Diffusion Map vignette with the supplied data()	HTML	R Script
destiny main vignette: Start here!	HTML	R Script
destiny 2.0 brought the Diffusion Pseudo Time (DPT) class	HTML	R Script
detecting relevant genes with destiny 3	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
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, CellBiology, Clustering, Software, Visualization
Version	3.27.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 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, scales, scatterplot3d
System Requirements	C++11
URL	https://github.com/theislab/destiny/ https://bioconductor.org/packages/destiny https://doi.org/10.1093/bioinformatics/btv715
Bug Reports	https://github.com/theislab/destiny/issues

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	dandelionR
Suggests Me	CellTrails, monocle
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	destiny_3.27.0.tar.gz
Windows Binary (x86_64)	destiny_3.27.0.zip
macOS Binary (big-sur-x86_64)	destiny_3.27.0.tgz
macOS Binary (sonoma-arm64)	destiny_3.27.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/destiny
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/destiny
Package Short Url	https://bioconductor.org/packages/destiny/
Package Downloads Report	Download Stats