About scDesign3Py

The R package scDesign3 is an all-in-one single-cell data simulation tool by using reference datasets with different cell states (cell types, trajectories or and spatial coordinates), different modalities (gene expression, chromatin accessibility, protein abundance, DNA methylation, etc), and complex experimental designs. The transparent parameters enable users to alter models as needed; the model evaluation metrics (AIC, BIC) and convenient visualization function help users select models.

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).

scDesign3Py is the python interface for the R package scDesign3, enabling python users to easily use the scDesign3 functions. scDesign3Py is developed based on rpy2.