destiny
Creates diffusion maps
Bioconductor version: Release (3.19)
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 "4.4") 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")| 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 | 3.18.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 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, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d |
| System Requirements | C++11 |
| 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 | knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr |
| Linking To | Rcpp, RcppEigen, grDevices |
| Enhances | rgl, SingleCellExperiment |
| Depends On Me | |
| Imports Me | |
| Suggests Me | CellTrails, CelliD, monocle |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | destiny_3.18.0.tar.gz |
| Windows Binary (x86_64) | destiny_3.18.0.zip |
| macOS Binary (x86_64) | destiny_3.18.0.tgz |
| macOS Binary (arm64) | destiny_3.18.0.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 |