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Hierarchical Annotation

Marker-based hierarchical gating with multi-level scoring. Configure for any tissue via JSON marker maps.

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Iterative Refinement

Policy-based refinement with automatic and manual modes. Subcluster, merge, and override operations with full provenance.

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Spatial Analysis

Neighborhood enrichment, Moran's I, and cell-type interactions. Permutation-based statistical tests with FDR correction.

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Composition Metrics

Shannon diversity, regional enrichment, and tissue-specific biology metrics with comprehensive export formats.