scDesign3

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

Bioconductor version: 3.23 · Package version: 1.10.0

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scDesign3")