scDesign3
This is the development version of scDesign3; for the stable release version, see scDesign3.
A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Bioconductor version: Development (3.21)
We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.
Author: Dongyuan Song [aut, cre] (ORCID:
Maintainer: Dongyuan Song <dongyuansong at ucla.edu>
citation("scDesign3")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scDesign3")
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("scDesign3")| scDesign3-quickstart-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Sequencing, SingleCell, Software, Spatial |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop |
| System Requirements | |
| URL | https://github.com/SONGDONGYUAN1994/scDesign3 |
| Bug Reports | https://github.com/SONGDONGYUAN1994/scDesign3/issues |
See More
| Suggests | mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scDesign3_1.5.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scDesign3 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scDesign3 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scDesign3/ |
| Package Short Url | https://bioconductor.org/packages/scDesign3/ |
| Package Downloads Report | Download Stats |