ArticleGenome biology2025
sCCIgen: a high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- Deciphering microenvironmental heterogeneity by scalable Niche Guided Module Discovery.Communications biology · 2026Article
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7 authors.
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Abstract
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.
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