destiny

DOI: 10.18129/B9.bioc.destiny    

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

Creates diffusion maps

Bioconductor version: Development (3.16)

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 <phil.angerer at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("destiny")

 

HTML R Script destiny 2.0 brought the Diffusion Pseudo Time (DPT) class
HTML R Script destiny main vignette: Start here!
HTML R Script detecting relevant genes with destiny 3
HTML R Script Reproduce the Diffusion Map vignette with the supplied data()
HTML R Script The effects of a global vs. local kernel
HTML R Script tidyverse and ggplot integration with destiny
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBasedAssays, CellBiology, Clustering, Software, Visualization
Version 3.11.0
In Bioconductor since BioC 3.2 (R-3.2) (6.5 years)
License GPL-3
Depends R (>= 3.4.0)
Imports methods, graphics, grDevices, grid, 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 knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr
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 CytoTree
Suggests Me CelliD, CellTrails, monocle
Links To Me
Build Report  

Package Archives

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

Source Package destiny_3.11.0.tar.gz
Windows Binary destiny_3.11.0.zip (64-bit only)
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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