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概要と使いどころ
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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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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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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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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Extracts and assigns COSMIC v3.4 mutational signatures (84 SBS / 11 DBS / 18 ID / 24 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.
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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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Provides JWT authentication and authorization patterns for Spring Boot 3.5.x covering token generation with JJWT, Bearer/cookie authentication, database/OAuth2 integration, and RBAC/permission-based access control using Spring Security 6.x. Use when implementing authentication or authorization in Spring Boot applications.
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Audits Hibernate database interactions to prevent N+1 query problems in JVM apps.
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Provides and generates complete CRUD workflows for Spring Boot 3 services. Creates feature-focused architecture with Spring Data JPA aggregates, repositories, DTOs, controllers, and REST APIs. Validates domain invariants and transaction boundaries. Use when modeling Java backend services, REST API endpoints, database operations, web service patterns, or JPA entities for Spring Boot applications.
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Run the database migration workflow for schema/data changes, operational sequencing, tests, and review.
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Use when working with @Transactional, multi-step database operations, distributed transactions, or any code that needs atomicity guarantees. Covers propagation rules, isolation levels, read-only optimization, and common pitfalls.
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Build reactive, type-safe, production-grade backends. ALWAYS use this skill when the user asks to build, plan, design, or implement backend features, APIs, data models, server logic, database schemas, web apps, full stack apps, or mobile apps. This includes planning and architecture discussions.
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Design and generate Convex database schemas with proper validation, indexes, and relationships. Use when creating schema.ts or modifying table definitions.
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Use this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants to: open, read, edit, or fix an existing .xlsx, .xlsm, .xltx, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting, charting, cleaning messy data); create a new spreadsheet from scratch or from other data sources; or convert between tabular file formats. Trigger especially when the user references a spreadsheet file by name or path — even casually (like "the xlsx in my downloads") — and wants something done to it or produced from it. Also trigger for cleaning or restructuring messy tabular data files (malformed rows, misplaced headers, junk data) into proper spreadsheets. The deliverable must be a spreadsheet file. Do NOT trigger when the primary deliverable is a Word document, HTML report, standalone Python script, database pipeline, or Google Sheets API integration, even if tabular data is involved.
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Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.
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You are a senior backend engineer operating production-grade services under strict architectural and reliability constraints. Use when routes, controllers, services, repositories, express middleware, or prisma database access.
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Azure PostgreSQL Flexible Server SDK for .NET. Database management for PostgreSQL Flexible Server deployments.
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Azure MySQL Flexible Server SDK for .NET. Database management for MySQL Flexible Server deployments.
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Connect to Azure Database for PostgreSQL Flexible Server from Node.js/TypeScript using the pg (node-postgres) package.
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Azure Cosmos DB SDK for Java. NoSQL database operations with global distribution, multi-model support, and reactive patterns.
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Deploy web apps with backend APIs, database, and file storage. Use when the user asks to deploy or publish a website or web app and wants a public URL. Uses HTTP API via curl.
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Android data layer implementation guide. Provides comprehensive patterns for Room Database (Entity, DAO, Migration), DataStore (Preferences), Repository layer design, and common pitfalls. Use when implementing local data storage, cache strategies, or data source integration in Android projects.
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Use when the user asks about the pwdev-prd audit trail — 'auditoria do prd', 'eventos', 'decisões registradas', 'audit report', 'exportar relatório de auditoria' — querying the shared SQLite database read-only (summary, events, decisions, artifacts, stats, export, query).
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Use when the user wants a UI-only action plan — components, pages, composables/hooks, state, forms and their E2E coverage — 'plano de frontend para a tela X', 'plan the settings page'. Writes .planning/feat/features/{slug}/plan.md with E2E scenarios and playwright-cli checks. Do NOT use for API/database work (feat-backend), full features (feat-feature), writing code (feat-exec) or UI review (feat-review).
日本語の概要は準備中です。原文の説明を表示しています。