destiny
This is thereleased version of destiny; for the devel version, seedestiny.
Creates diffusion maps
Bioconductor version: Release (3.22)
Create and plot diffusion maps.
Author: Philipp Angerer [cre, aut]
ORCID: 0000-0002-0369-2888, Laleh Haghverdi [ctb], Maren Büttner [ctb] ORCID: 0000-0002-6189-3792, Fabian Theis [ctb] ORCID: 0000-0002-2419-1943, Carsten Marr [ctb] ORCID: 0000-0003-2154-4552, Florian Büttner [ctb] ORCID: 0000-0001-5587-6761
Maintainer: Philipp Angerer <phil.angerer at gmail.com>
citation("destiny")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("destiny")For older versions of R, please refer to the appropriateBioconductor 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 | 3.24.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (10 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/destinyhttps://bioconductor.org/packages/destinyhttps://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 | dandelionR |
| Suggests Me | CelliD,CellTrails,monocle |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | destiny_3.24.0.tar.gz |
| Windows Binary (x86_64) | destiny_3.24.0.zip (64-bit only) |
| macOS Binary (x86_64) | destiny_3.24.0.tgz |
| macOS Binary (arm64) | destiny_3.24.0.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 |