Results for “database”

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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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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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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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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S3, multipart uploads, CDN integration, and presigned URLs for file storage. Activate on: file upload, S3, presigned URL, multipart upload, CDN, blob storage, image upload, media storage. NOT for: data warehouse storage (use lakehouse-architect), database design (use dimensional-modeler).

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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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Expert DevOps engineer for CI/CD, IaC, Kubernetes, and deployment automation. Activate on: CI/CD, GitHub Actions, Terraform, Docker, Kubernetes, Helm, ArgoCD, GitOps, deployment pipeline, infrastructure as code, container orchestration. NOT for: application code (use language skills), database schema (use data-pipeline-engineer), API design (use api-architect).

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Large-scale data migrations with validation, rollback, and zero-downtime strategies. Activate on: data migration, database migration, zero-downtime migration, dual-write, backfill, cutover, data validation, schema migration. NOT for: schema evolution in streams (use schema-evolution-manager), API versioning (use api-versioning-backward-compatibility).

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Use when applying Cloudflare D1 migrations, fighting Supabase migration history vs SQL execution, choosing direct psql over CLI, designing idempotent migrations, debugging schema drift between local and remote, or recovering after a half-applied migration. Triggers: supabase migration repair instructions appearing, table missing after "applied" status, "Tenant or user not found" when running psql, --remote vs --local D1 confusion, NOT NULL on a populated column, foreign key constraint failures, drift between staging and prod schemas. NOT for Mongo/document migrations, ORM-managed migrations specifically (Prisma/Drizzle have their own conventions), or pure data backfills.

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Building resilient distributed systems with circuit breakers, retries with full-jitter exponential backoff, retry budgets (per-request 3-attempt + per-client 10% ratio per Google SRE), deadline propagation, and the cascading-failure math (4 layers × 3 retries = 64x amplification). Grounded in Resilience4j, Microsoft Cloud Patterns, AWS Architecture Blog (Marc Brooker), and Google SRE Book. NOT for server-side rate limiting, bulkhead isolation, backpressure protocols, or database-specific retry.

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CQRS pattern, event stores, projections, eventual consistency. Activate on: CQRS, event sourcing, event store, read model, projection, aggregate, domain event, command handler. NOT for: message broker setup (use event-driven-architecture-expert), database optimization (use data-warehouse-optimizer).

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Redis caching patterns, cache-aside, write-through, TTL strategies, and invalidation. Activate on: caching, Redis, cache invalidation, cache-aside, write-through, TTL, CDN cache, stale-while-revalidate. NOT for: CDN/reverse proxy setup (use api-gateway-reverse-proxy-expert), database query optimization (use data-warehouse-optimizer).

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Design multi-tier caching architectures for web applications — cache-aside vs write-through vs write-behind, TTL design, cache invalidation, Redis patterns, CDN configuration, browser caching, and stampede prevention. Use when choosing a caching pattern, designing cache invalidation strategies, implementing Redis caching, configuring Cache-Control headers, or preventing cache stampedes. Activate on "cache invalidation", "cache-aside", "write-through", "TTL", "Redis cache", "CDN caching", "cache stampede", "stale data", "browser cache". NOT for database query caching within an ORM, memoization of pure functions, or CPU-level caching.

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Expert API designer for REST, GraphQL, gRPC architectures. Activate on: API design, REST API, GraphQL schema, gRPC service, OpenAPI, Swagger, API versioning, endpoint design, rate limiting, OAuth flow. NOT for: database schema (use data-pipeline-engineer), frontend consumption (use web-design-expert), deployment (use devops-automator).

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Choosing and operating an HTTP API versioning strategy that doesn't break clients — Stripe's date-based pinned versions, the Deprecation/Sunset header pair (RFC 9745 + RFC 8594), URI vs header vs media-type approaches, and the version-transformer pattern. Grounded in Stripe's published architecture and IETF RFCs. NOT for GraphQL schema evolution, gRPC/Protobuf wire compatibility, database schema migrations, or library/SDK semver.

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Moves a person's whole Notion workspace into AI Matrx using only the AI Matrx and Notion connectors — every page and sub-page becomes an AI Matrx page (a Space) with its blocks, icons, covers, files and comments, and every database becomes a real table with typed columns, links, roll-ups, row pages, templates and views. Safe to run again; nothing duplicates. Use when the person says "move my Notion into AI Matrx", "copy my Notion", "import my Notion", or anything like it.

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Scaffold recipe for a new authenticated route: SSR shell, DB-derived types, Redux hydration, view sub-pages. Use when creating a new route or page, adding a feature with a sidebar/main layout, adding view modes to a route, or feature types don't match database.types.ts.

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Entry point and shared rules for structural changes to the live Matrx database. Use before any DDL: dropping, merging, or renaming a table, changing a function, RPC, trigger, or policy, hunting straggler tables, or starting a deprecated, schema move, or canonicalization (it routes to those skills).

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PostgreSQL、MySQL、および一般的なORM（Prisma、Drizzle、Kysely、Django、TypeORM、golang-migrate）にわたるスキーマ変更、データマイグレーション、ロールバック、ゼロダウンタイムデプロイメントのためのデータベースマイグレーションベストプラクティス。

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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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Seed or import data into the Convex database.

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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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Generates PHPUnit integration tests for PHP 8.5. Creates tests with real dependencies, database transactions, HTTP mocking. Supports repositories, API clients, message handlers.

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Generates InMemory repository implementations for PHP 8.5 testing. Creates fake repositories with array storage, supporting CRUD operations and queries without database.

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