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generic-phenotype-scoring-research-planner

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Generates complete phenotype-scoring bioinformatics research designs for any disease context and any user-defined phenotype, pathway, process, signature, or molecular program. Use when a study centers on gene-set or feature-set definition, intersection with DEGs or candidate features, phenotype scoring, feature selection, diagnostic or stratification assessment, immune or cellular-resolution interpretation, network analysis, and optional orthogonal validation. Covers five study patterns (signature discovery, phenotype scoring, feature selection, immune/cellular interpretation, multi-layer validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

When to use

• gene-set or feature-set definition
• intersection with DEGs or candidate features
• phenotype scoring
• feature selection
• diagnostic or stratification assessment
• immune or cellular-resolution interpretation
• network analysis
• orthogonal validation

When not to use

• clinical treatment recommendations
• patient-specific diagnosis
• prescribing
• pure single-cell-only studies with no bulk discovery backbone
• pure wet-lab mechanistic studies with no bioinformatics integration
• standard prognostic-model papers with no phenotype-scoring or signature backbone
• non-biomedical / off-topic requests

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