destiny

DOI: 10.18129/B9.bioc.destiny    

Creates diffusion maps

Bioconductor version: Release (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>

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

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 3.0.0
In Bioconductor since BioC 3.2 (R-3.2) (4 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, igraph, testthat, FNN, tidyr
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 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_3.0.0.tar.gz
Windows Binary destiny_3.0.0.zip
Mac OS X 10.11 (El Capitan)
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 3.10 Source Archive

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