scDesign3Py: python interface for scDesign3 R package

The R package scDesign3 is a unified probabilistic framework that generates realistic in silico high-dimensional single-cell omics data of various cell states, including discrete cell types, continuous trajectories, and spatial locations by learning from real datasets.

scDesign3Py is the python interface of the R package scDesign3, enabling python users to easily use the scDesign3 functions and share almost the same usage as the R version.

Summary of usage of scDesign3

To find out more details about scDesign3, you can check out manuscript on Nature Biotechnology:

Song, D., Wang, Q., Yan, G. et al. scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics. Nat Biotechnol (2023).

For tutorial of R package scDesign3, you can check the tutorial website.

Get Started

• Installation
• API
• Quick Start
• About scDesign3Py

Tutorial

• All in one simulation
• Step by step simulation
• Get BPPARAM
• Perform likelihood ratio test
• Plot results

More examples

• Model parameter
• Data simulation
• Model selection
• Model alteration