destiny

DOI: 10.18129/B9.bioc.destiny    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see destiny.

Creates diffusion maps

Bioconductor version: 3.12

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 <philipp.angerer at helmholtz-muenchen.de>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF		Diffusion-Map-recap.pdf
PDF		Diffusion-Maps.pdf
PDF		DPT.pdf
PDF		Gene-Relevance.pdf
PDF		Global-Sigma.pdf
PDF		tidyverse.pdf
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, CellBiology, Clustering, Software, Visualization
Version	3.4.0
In Bioconductor since	BioC 3.2 (R-3.2) (5.5 years)
License	GPL
Depends	R (>= 3.4.0)
Imports	methods, graphics, grDevices, 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	nbconvertR (>= 1.3.2), igraph, testthat, FNN, tidyr
SystemRequirements	C++11, jupyter nbconvert (see nbconvertR’s INSTALL file)
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	ctgGEM, CytoTree, flowSpy, phemd
Suggests Me	CellTrails, monocle, scater
Links To Me
Build Report

Package Archives

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

Source Package	destiny_3.4.0.tar.gz
Windows Binary	destiny_3.4.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
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