destiny
Creates diffusion maps
Bioconductor version: 3.23 · Package version: 3.26.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Create and plot diffusion maps.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("destiny")Details
| Maintainer | Philipp Angerer <phil.angerer@gmail.com> |
| Author | Philipp Angerer [cre, aut] (ORCID: <https://orcid.org/0000-0002-0369-2888>), Laleh Haghverdi [ctb], Maren Büttner [ctb] (ORCID: <https://orcid.org/0000-0002-6189-3792>), Fabian Theis [ctb] (ORCID: <https://orcid.org/0000-0002-2419-1943>), Carsten Marr [ctb] (ORCID: <https://orcid.org/0000-0003-2154-4552>), Florian Büttner [ctb] (ORCID: <https://orcid.org/0000-0001-5587-6761>) |
| License | GPL-3 |
| 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 |
| System Requirements | C++11 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | CellBasedAssays, CellBiology, Clustering, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/destiny/ |
Citation
From within R, enter citation("destiny"):
Philipp Angerer. destiny: Creates diffusion maps. doi:10.18129/B9.bioc.destiny, R package version 3.26.0, https://bioconductor.org/packages/destiny.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- destiny 2.0 brought the Diffusion Pseudo Time (DPT) class
- destiny main vignette: Start here!
- detecting relevant genes with destiny 3
- Reproduce the Diffusion Map vignette with the supplied data()
- The effects of a global vs. local kernel
- tidyverse and ggplot integration with destiny
Download
Follow the 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 (arm64) | destiny_3.26.0.tgz |
| macOS binary (x86_64) | destiny_3.26.0.tgz |
Dependencies
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
LinkingTo: Rcpp, RcppEigen, grDevices
Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr
Enhances: rgl, SingleCellExperiment