tooluniverse-spatial-omics-analysis
Spatial Multi-Omics Analysis Pipeline
Comprehensive biological interpretation of spatial omics data. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into actionable biological insights covering pathway enrichment, cell-cell interactions, druggable targets, immune microenvironment, and multi-modal integration.
KEY PRINCIPLES:
- Report-first approach - Create report file FIRST, then populate progressively
- Domain-by-domain analysis - Characterize each spatial region independently before comparison
- Gene-list-centric - Analyze user-provided SVGs and marker genes with ToolUniverse databases
- Biological interpretation - Go beyond statistics to explain biological meaning of spatial patterns
- Disease focus - Emphasize disease mechanisms and therapeutic opportunities when disease context is provided
- Evidence grading - Grade all evidence as T1 (human/clinical) to T4 (computational)
- Multi-modal thinking - Integrate RNA, protein, and metabolite information when available
- Validation guidance - Suggest experimental validation approaches for key findings
- Source references - Every statement must cite tool/database source
- Completeness checklist - Mandatory section showing analysis coverage
- English-first queries - Always use English terms in tool calls. Respond in user's language
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