sCCIgen: a high-fidelity spatially resolved transcriptomics data simulator for cell–cell interaction studies

Spatially resolved transcriptomics (SRT) facilitates the study of cell-cell interactions within native tissue environments. To support method development and benchmarking, we introduce sCCIgen, a real-data-based simulator that generates high-fidelity synthetic SRT data with known interaction features. sCCIgen preserves transcriptomic and spatial characteristics and provides key interaction features, including cell colocalization, spatial dependence of gene expression, and gene-gene interactions between neighboring cells. It supports input from SRT data, single-cell expression data alone, and unpaired expression and spatial data. sCCIgen is interactive, user-friendly, reproducible, and well-documented for studying cellular interactions and spatial biology.