271 skills · sorted by relevance
Phase 2 of disease-market-sizing-orchestration. Discovers disease-specific stratification dimensions by citing guideline sections from sources/guidelines/. ALWAYS uses cite-based discovery — NEVER built-in stratification templates. Output: .cache/<slug>/staging.json. Use AFTER contract-elicitor and AFTER A1' guidelines fetch.
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Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning with mechanism rationale, clinical-trial precedent, and patent/regulatory feasibility. Use for hypothesis-generating repurposing for orphan diseases, finding existing drugs for new indications, and prioritizing candidates by evidence and feasibility.
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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.
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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.
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Support drug discovery research by searching public databases for compound activity, molecular properties, drug interactions, and gene–disease associations. Assess drug-likeness, meaning how molecular properties fit established rules for potential oral medicines.
Look up genes, sequences, protein structures, expression patterns, and disease associations across more than 20 bioinformatics resources using command-line tools or Python. Useful for interactive exploration, with results that can be saved for further analysis.
Query public single-cell and spatial gene expression data by tissue, disease, or cell type. Retrieve selected expression values, cell metadata, and summary counts for analysis and comparisons across datasets without first downloading entire collections.
Turn broad life sciences questions into focused research plans. Resolve names and identifiers for genes, diseases, or compounds, select relevant research skills, and combine evidence into a concise answer that explains uncertainty and useful follow-up analyses.
Look up one genetic variant in BioBank Japan and get a concise summary of its associations with diseases and traits. Accepts rsIDs or genome coordinates, converts the query as needed, and can save complete results.
Build a structured research dossier for a defined patient population, covering epidemiology, disease biology, current treatment, regulatory precedents, and major clinical trials. Receive a cited report and structured data to inform therapeutic development and trial planning.
Search NIH Metabolomics Workbench for metabolite structures, study details, and experimental data. Standardize metabolite names with RefMet, find candidate compounds from mass spectrometry measurements, and filter studies by disease, sample source, or analytical method.
Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.
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Performs epidemiological analyses including disease modeling (SIR/SEIR), outbreak investigation, risk factor identification, incidence/prevalence estimation, and causal inference from observational data; trigger when users discuss disease spread, public health data, or populat...
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Generates complete conventional non-oncology diagnostic machine-learning research designs from a user-provided disease context, optional mechanism theme, and validation direction. Use when a study centers on disease-vs-control transcriptome comparison, optional mechanism-gene restriction, feature shrinkage, diagnostic model construction, ROC / calibration / DCA evaluation, interpretation layers, and orthogonal validation. Covers five study patterns 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.
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Generates complete comorbidity-oriented shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction. Use when a study links two clinically related diseases through shared DEGs, enrichment, PPI hub genes, machine-learning feature selection, public diagnostic validation, gene-regulatory networks, immune infiltration, and optional downstream follow-up. Covers five study patterns (shared-DEG discovery, hub-gene prioritization, machine-learning biomarker selection, immune/regulatory 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.
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Generates complete NHANES-style cross-sectional epidemiology + retrospective clinical validation research designs from a user-provided disease and biomarker direction. Always use this skill whenever a user wants to design, plan, or build a population-level biomarker association study using NHANES or similar survey datasets, especially when the article logic includes disease definition, biomarker formula derivation, multivariable logistic regression, restricted cubic spline analysis, subgroup stability testing, and a secondary hospital-based retrospective validation cohort. Covers five study patterns (cross-sectional association, dose-response / RCS, subgroup-stability, NHANES + retrospective validation, preliminary screening-performance) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path...
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Systematically maps mechanism evidence for a disease from molecules to pathways, cell types, tissues, biological consequences, and clinical phenotypes. Always use this skill when a user needs a layered mechanism evidence chain rather than a flat summary or immediate gap analysis. Formal literature citations must be real and verifiable.
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Evidence-based medical knowledge and research mentor grounded in the Bian Que tradition. Covers clinical reasoning, diagnostic thinking (望闻问切), pharmacology, pathology, differential diagnosis, medical literature appraisal, and the philosophy of early intervention. Trigger whenever users ask about medicine, clinical science, drugs, disease mechanisms, diagnosis, lab interpretation, treatment comparison, or health sciences. Even without explicit research framing, trigger on any topic touching disease, therapeutics, or clinical decision-making. Part of the AIPOCH Medical Research Skill Hub.
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Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for multi-DB Python SDK use bioservices.
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Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene, diseases by EFO ID; scores from 20+ sources, drug mechanisms, tractability. For ChEMBL use chembl-database-bioactivity; for trials use clinicaltrials-database-search.
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Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".
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🔨 Andru.ia Skill-Smith (The Forge) workflow skill. Use this skill when the user needs Ingeniero de Sistemas de Andru.ia. Diseña, redacta y despliega nuevas habilidades (skills) dentro del repositorio siguiendo el Estándar de Diamante and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
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🔨 Andru.ia Skill-Smith (The Forge) workflow skill. Use this skill when the user needs Ingeniero de Sistemas de Andru.ia. Diseña, redacta y despliega nuevas habilidades (skills) dentro del repositorio siguiendo el Estándar de Diamante and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
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Applies the epidemiological reasoning and population-health frameworks of Albert Hofman (Harvard epidemiologist, Rotterdam Study). Trigger this skill whenever you are analyzing public health strategies, preventive medicine, cohort study design, cardiovascular or neurodegenerative disease risks, or healthy aging. Use it when evaluating whether to use population-wide interventions versus individual screening, assessing risk factors in elderly populations, or tracing adult chronic diseases back to early-life or fetal origins.
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