Welcome to the new bioconductor.org!


A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics

Bioconductor version: Release (3.18)

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] , Qingyang Wang [aut]

Maintainer: Dongyuan Song <dongyuansong at ucla.edu>

Citation (from within R, enter citation("scDesign3")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

scDesign3-quickstart-vignette HTML R Script
Reference Manual PDF


biocViews GeneExpression, Sequencing, SingleCell, Software, Spatial
Version 1.0.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix
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
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_1.0.1.tar.gz
Windows Binary scDesign3_1.0.1.zip (64-bit only)
macOS Binary (x86_64) scDesign3_1.0.1.tgz
macOS Binary (arm64) scDesign3_1.0.1.tgz
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
Old Source Packages for BioC 3.18 Source Archive