destiny

DOI: 10.18129/B9.bioc.destiny    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

Creates diffusion maps

Bioconductor version: Development (3.14)

Create and plot diffusion maps.

Author: Philipp Angerer <philipp.angerer at helmholtz-muenchen.de>, Laleh Haghverdi <laleh.haghverdi at helmholtz-muenchen.de>, Maren Büttner <maren.buettner at helmholtz-muenchen.de>, Fabian Theis <fabian.theis at helmholtz-muenchen.de>, Carsten Marr <carsten.marr at helmholtz-muenchen.de>, Florian Büttner <f.buettner at helmholtz-muenchen.de>

Maintainer: Philipp Angerer <philipp.angerer at helmholtz-muenchen.de>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("destiny")

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

Documentation

PDF   Reference Manual

Details

biocViews CellBasedAssays, CellBiology, Clustering, Software, Visualization
Version 3.7.1
In Bioconductor since BioC 3.2 (R-3.2) (6 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 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
Windows Binary
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

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