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

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DOI: 10.18129/B9.bioc.scDesign3

Bioconductor version: Development (3.23)

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 iD ORCID: 0000-0003-1114-1215 , Qingyang Wang [aut] ORCID iD ORCID: 0000-0002-1051-609X , Chenxin Jiang [aut] ORCID iD ORCID: 0009-0005-7369-4116

Maintainer: Dongyuan Song <dongyuansong at ucla.edu>

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

Installation

To install this package, start R (version "4.6") 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.