destiny

DOI: 10.18129/B9.bioc.destiny    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see destiny.

Creates diffusion maps

Bioconductor version: 3.10

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 "3.6") 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	3.0.1
In Bioconductor since	BioC 3.2 (R-3.2) (4.5 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	flowSpy, phemd
Suggests Me	CellTrails, monocle, scater, slingshot
Links To Me
Build Report

Package Archives

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

Source Package	destiny_3.0.1.tar.gz
Windows Binary	destiny_3.0.1.zip
Mac OS X 10.11 (El Capitan)	destiny_3.0.1.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