destiny
This is the released version of destiny; for the devel version, see destiny.
Creates diffusion maps
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 3.26.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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, scales, scatterplot3d |
| System Requirements | C++11 |
| URL | https://github.com/theislab/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 | dandelionR |
| Suggests Me | CelliD, CellTrails, monocle |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | destiny_3.26.0.tar.gz |
| Windows Binary (x86_64) | destiny_3.26.0.zip |
| macOS Binary (big-sur-x86_64) | destiny_3.26.0.tgz |
| macOS Binary (sonoma-arm64) | destiny_3.26.0.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 |