scCircaSim: A Circadian Simulator for Single-Cell and Spatial Transcriptomics

scCircaSim generates circadian single-cell and spatial transcriptomic datasets from a single-time-point reference, outputting known cell/spot phases and gene mesor, amplitude, and phase.

• Why it matters: Ground-truth circadian simulations for single-cell and spatial data are scarce, which limits systematic evaluation of circadian analysis methods and planning of experiments.
• What they did: The framework advances phase progression using reference-derived network propagation of anchor gene rhythms and adds spatial neighborhood effects to simulate spatial transcriptomics.
• The result: Validation showed retention of reference structure and recovery of specified temporal patterns, and benchmarks across four phase inference and three rhythmicity methods quantified differences in phase accuracy, detection, and parameter recovery.

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