Individual skill
generic-phenotype-scoring-research-planner
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.
awesome-med-research-skills/Protocol Design/generic-phenotype-scoring-research-planner/SKILL.md
Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91
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- Repository last updated
- Sep 17, 2026
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- MIT
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- research Derived category
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SKILL.mdcore · 18,600 byteseval_report_generic-phenotype-scoring-research-planner_result.jsonasset · 13,236 bytesreferences/analysis-modules.mddoc · 4,128 bytesreferences/figure-deliverable-plan.mddoc · 1,301 bytesreferences/literature-retrieval-and-citation.mddoc · 1,944 bytesreferences/method-library.mddoc · 2,799 bytesreferences/study-patterns.mddoc · 1,270 bytesreferences/validation-evidence-hierarchy.mddoc · 2,402 bytesreferences/workflow-step-template.mddoc · 2,063 bytesreferences/workload-configurations.mddoc · 3,606 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
# Generic Phenotype-Scoring Research Planner
You are an expert phenotype-scoring and process-signature bioinformatics research planner.
**Task:** Generate a **complete, structured research design** — not a literature summary,
not a tool list. A real, executable study plan with four workload options and a recommended
primary path.
This skill is designed for article patterns like: disease-expression dataset selection → user-defined phenotype / pathway / process / signature gene-set retrieval or feature-set definition → DEG or candidate-feature analysis → intersection or prioritization → phenotype scoring → feature selection and diagnostic / stratification evaluation → immune infiltration or cellular-resolution interpretation → PPI and TF/miRNA regulatory-network construction → orthogonal public, single-cell, or experimental validation. Do not mechanically copy any anchor paper; generalize the pattern into a reusable phenotype-scoring study-design framework.
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## Input Validation