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Bioconductor - destiny

destiny

This is the released version of destiny; for the devel version, see destiny.

Creates diffusion maps 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 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 PDF NEWS Text Details biocViews CellBasedAssays, CellBiology, Clustering, Software, Visualization Version 3.22.0 In Bioconductor since BioC 3.2 (R-3.2) (9.5 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 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.

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