Results for “databases”

Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), MSIngs, MANTIS, MSIPanel, MSIDetect, and ngsMSI for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

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Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, HLA-LA, T1K, Polysolver, HLA-HD, arcasHLA, StarPhase, or HIBAG imputation. Use when typing for HSCT, solid-organ transplant, neoantigen prediction, PGx screening (B*57:01, B*15:02, etc.), or disease-association studies, with reconciliation across tools and IPD-IMGT/HLA version mismatch handling.

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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.

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Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).

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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA pembrolizumab pan-tumor 2020.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Schema design, normalization decisions, indexing strategies, and migration safety for relational databases. Use when designing tables, choosing between normalize vs denormalize, selecting index types, planning zero-downtime migrations, or setting up connection pooling. Activate on "schema design", "normalization", "denormalization", "foreign key", "index strategy", "migration", "connection pooling", "composite key", "surrogate key", "soft delete", "polymorphic association". NOT for PostgreSQL-specific query tuning or EXPLAIN analysis (use postgresql-optimization), NoSQL or document database design, or cloud database provisioning.

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Long-running design anthropologist that builds comprehensive visual databases from 500-1000 real-world examples, extracting color palettes, typography patterns, layout systems, and interaction design across any domain (portfolios, e-commerce, SaaS, adult content, technical showcases). This skill should be used when users need exhaustive design research, pattern recognition across large example sets, or systematic visual analysis for competitive positioning.

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Write academic research documents following academic guidelines with peer-reviewed sources from Google Scholar and other academic databases. Always verify source credibility and generate IEEE standard references. Use for research papers, literature reviews, technical reports, theses, dissertations, conference papers, and academic proposals requiring proper citations and scholarly rigor.

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Connect Claude to any app. Send emails, create issues, post messages, update databases - take real actions across Gmail, Slack, GitHub, Notion, and 1000+ services.

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Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.

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Searchable UI/UX design databases: 50+ styles, 97 palettes, 57 font pairings, 99 UX rules, 25 chart types. CLI generates design systems from natural language. Data-driven complement to ui-design.

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Conduct deep, multi-source research by cross-referencing data from web search, news, social media, academic sources, and proprietary databases. Enforces APA 7th citations, evidence hierarchy, and 2-cycle verification per research theme. Built for competitive intelligence analyst workflows.

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Build and ship software — code, implement, develop, API, backend, frontend, deploy, infrastructure, CI/CD, databases, cloud, mobile, AI/ML. The CTO office's broadest execution domain, applied with TDD discipline.

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Fetches real-time Azure retail pricing using the Azure Retail Prices API (prices.azure.com) and estimates Copilot Studio agent credit consumption. Use when the user asks about the cost of any Azure service, wants to compare SKU prices, needs pricing data for a cost estimate, mentions Azure pricing, Azure costs, Azure billing, or asks about Copilot Studio pricing, Copilot Credits, or agent usage estimation. Covers compute, storage, networking, databases, AI, Copilot Studio, and all other Azure service families.

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Patterns and techniques for adding governance, safety, and trust controls to AI agent systems. Use this skill when: - Building AI agents that call external tools (APIs, databases, file systems) - Implementing policy-based access controls for agent tool usage - Adding semantic intent classification to detect dangerous prompts - Creating trust scoring systems for multi-agent workflows - Building audit trails for agent actions and decisions - Enforcing rate limits, content filters, or tool restrictions on agents - Working with any agent framework (PydanticAI, CrewAI, OpenAI Agents, LangChain, AutoGen)

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Notion API + ntn CLI: pages, databases, markdown, Workers.

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Master modern SQL with cloud-native databases, OLTP/OLAP optimization, and advanced query techniques. Expert in performance tuning, data modeling, and hybrid analytical systems. Use PROACTIVELY for database optimization or complex analysis.

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Expert in vector databases, embedding strategies, and semantic search implementation. Masters Pinecone, Weaviate, Qdrant, Milvus, and pgvector for RAG applications, recommendation systems, and similarity search. Use PROACTIVELY for vector search implementation, embedding optimization, or semantic retrieval systems.

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Elite AI context engineering specialist mastering dynamic context management, vector databases, knowledge graphs, and intelligent memory systems. Orchestrates context across multi-agent workflows, enterprise AI systems, and long-running projects with 2024/2025 best practices. Use PROACTIVELY for complex AI orchestration.

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Detect and exploit NoSQL injection vulnerabilities in MongoDB, CouchDB, and other NoSQL databases to demonstrate authentication bypass, data extraction, and unauthorized access risks.

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