destiny

DOI: 10.18129/B9.bioc.destiny    

Creates diffusion maps

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, CellBiology, Clustering, Software, Visualization
Version	3.8.1
In Bioconductor since	BioC 3.2 (R-3.2) (6.5 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
LinkingTo	Rcpp, RcppEigen, grDevices
Suggests	knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr
SystemRequirements	C++11
Enhances	rgl, SingleCellExperiment
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
BugReports	https://github.com/theislab/destiny/issues
Depends On Me
Imports Me	CytoTree, phemd
Suggests Me	CelliD, CellTrails, monocle, scater
Links To Me
Build Report

Package Archives

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

Source Package	destiny_3.8.1.tar.gz
Windows Binary	destiny_3.8.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	destiny_3.8.1.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
Old Source Packages for BioC 3.14	Source Archive