destiny
This is the development version of destiny; for the stable release version, see destiny.
Creates diffusion maps
Bioconductor version: Development (3.18)
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("destiny")
):
Installation
To install this package, start R (version "4.3") 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")
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 | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | CellBasedAssays, CellBiology, Clustering, Software, Visualization |
Version | 3.15.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (8 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 |
Linking To | Rcpp, RcppEigen, grDevices |
Suggests | knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr |
System Requirements | 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 |
Bug Reports | https://github.com/theislab/destiny/issues |
See More
Depends On Me | |
Imports Me | phemd |
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_3.15.0.tar.gz |
Windows Binary | destiny_3.15.0.zip (64-bit only) |
macOS Binary (x86_64) | destiny_3.15.0.tgz |
macOS Binary (arm64) | destiny_3.15.0.tgz |
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 |