sCCIgen

sCCIgen simulates high-fidelity spatially resolved transcriptomics (SRT) data with known interaction features to support method development and benchmarking for cell-cell interaction studies.

Key Features:

• Real-data-based simulation: sCCIgen generates synthetic SRT data based on real data inputs.
• Transcriptomic and spatial characteristic preservation: The simulator preserves both transcriptomic and spatial characteristics from input data.
• Interaction feature generation: sCCIgen provides key interaction features including cell colocalization, spatial dependence of gene expression, and gene-gene interactions between neighboring cells.
• Flexible input support: The tool supports input from SRT data, single-cell expression data alone, and unpaired expression and spatial data.

Scientific Applications:

• Cell-cell interaction method development: sCCIgen facilitates the development of computational methods for studying cell-cell interactions within native tissue environments.
• Benchmarking: The simulator enables benchmarking of methods for analyzing spatially resolved transcriptomics data with known ground truth interaction features.
• Spatial biology research: sCCIgen supports studies of cellular interactions and spatial biology through controlled synthetic data generation.

Methodology:

sCCIgen is a real-data-based simulator that generates synthetic SRT data with known interaction features.