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>

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

Installation

To install this package, start R (version "4.0") 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")
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 PDF
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, CellBiology, Clustering, Software, Visualization
Version 3.4.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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
System Requirements C++11, jupyter nbconvert (see nbconvertR’s INSTALL file)
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
Bug Reports https://github.com/theislab/destiny/issues
See More
Suggests nbconvertR (>= 1.3.2), igraph, testthat, FNN, tidyr
Linking To Rcpp, RcppEigen, grDevices
Enhances rgl, SingleCellExperiment
Depends On Me
Imports Me ctgGEM, CytoTree, flowSpy, phemd
Suggests Me CellTrails, monocle, scater
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/destiny/
Package Short Url https://bioconductor.org/packages/destiny/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive