「config」の検索結果

Read a liarjs fingerprint report and attribute each failing check to the component that produced it - what the check id measures, whether the signal comes from the launch configuration, the page-modifying layer, the network path or the machine image, and which failures are inherent to headless or datacenter environments. Use when a fingerprint scan came back with a low score, or when a check id such as webdriver, worker-consistency, gpu-triad, native-integrity or tz needs explaining.

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Calls significant loops from protein-directed and targeted 3C assays (HiChIP, PLAC-seq, Capture Hi-C/PCHi-C, ChIA-PET) where the contact background is peak-anchored and coverage-biased, so generic Hi-C loop callers (cooltools dots, Juicer HiCCUPS) use the wrong null. Covers FitHiChIP (config-driven coverage+distance-decay spline regression, peak-to-peak vs peak-to-all foreground, loose vs stringent background, coverage vs ICE bias), MAPS (positive Poisson regression on bias factors for PLAC-seq/HiChIP), hichipper (restriction-site-distance bias model + library QC), CHiCAGO (Delaporte two-component Brownian+technical background for asymmetric bait x other-end Capture Hi-C), the with/without separate-ChIP anchor decision, and differential loops via diffloop. Use when calling loops from HiChIP/PLAC-seq/Capture Hi-C, choosing FitHiChIP/MAPS/CHiCAGO, picking peak-to-all vs peak-to-peak, setting the loop FDR, supplying ChIP peaks as anchors, QCing a HiChIP library, or comparing loops between conditions.

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Provides Spring Data Neo4j integration patterns for Spring Boot applications. Use when you need to work with a graph database, Neo4j nodes and relationships, Cypher queries, or Spring Data Neo4j. Creates node entities with @Node annotation, defines relationships with @Relationship, writes Cypher queries using @Query, configures imperative and reactive Neo4j repositories, implements graph traversal patterns, and sets up testing with embedded databases.

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Provides patterns to generate comprehensive REST API documentation using SpringDoc OpenAPI 3.0 and Swagger UI in Spring Boot 3.x applications. Use when setting up API documentation, configuring Swagger UI, adding OpenAPI annotations, implementing security documentation, or enhancing REST endpoints with examples and schemas.

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Refactor Spring Boot and Java code to improve maintainability, readability, and adherence to enterprise best practices. This skill transforms messy Spring Boot applications into clean, well-structured solutions following SOLID principles and Spring Boot 3.x conventions. It addresses fat controllers, improper transaction boundaries, field injection anti-patterns, and scattered configuration. Leverages Java 21+ features including record patterns, pattern matching for switch, virtual threads, and sequenced collections.

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Provides dependency injection patterns for Spring Boot projects, including constructor-first design, optional collaborator handling, bean selection, and wiring validation. Use when creating services and configurations, replacing field injection, or troubleshooting ambiguous or fragile Spring wiring.

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Provides patterns to configure Spring Boot Actuator for production-grade monitoring, health probes, secured management endpoints, and Micrometer metrics across JVM services. Use when setting up monitoring, health checks, or metrics for Spring Boot applications.

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Provides Event-Driven Architecture (EDA) patterns for Spring Boot — creates domain events, configures ApplicationEvent and @TransactionalEventListener, sets up Kafka producers and consumers, and implements the transactional outbox pattern for reliable distributed messaging. Use when implementing event-driven systems in Spring Boot, setting up async messaging with Kafka, publishing domain events from DDD aggregates, or needing reliable event publishing with the outbox pattern.

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Spring Boot 3 patterns for configuration, DI, and web services. Trigger: When building or refactoring Spring Boot 3 applications.

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Use when building PHP applications with modern PHP 8.3+ features, Laravel, or Symfony frameworks. Invokes strict typing, PHPStan level 9, async patterns with Swoole, and PSR standards. Creates controllers, configures middleware, generates migrations, writes PHPUnit/Pest tests, defines typed DTOs and value objects, sets up dependency injection, and scaffolds REST/GraphQL APIs. Use when working with Eloquent, Doctrine, Composer, Psalm, ReactPHP, or any PHP API development.

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Use when implementing authentication, authorization, JWT tokens, security filters, password encoding, or any Spring Security configuration. Covers stateless JWT auth, token rotation, RBAC, and method-level security.

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Use when generating or modifying any Spring Boot class — controllers, services, repositories, DTOs, mappers, or configuration. Enforces strict layer separation and prevents business logic from leaking across boundaries.

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Use when configuring Spring Boot as an OAuth2 resource server, validating JWTs from an external auth provider (Keycloak, Auth0, Okta, Cognito), extracting claims, or implementing scope-based authorization.

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Debug Spring Boot issues systematically. Use when encountering bean errors like NoSuchBeanDefinitionException, circular dependency issues, application startup failures, JPA/Hibernate problems including LazyInitializationException and N+1 queries, security misconfigurations causing 403 Forbidden errors, property binding failures, CSRF token issues, or any Spring Boot application requiring diagnosis with Actuator endpoints and JVM debugging.

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Use when implementing caching, session storage, rate limiting, or any Redis integration. Covers cache-aside pattern, key naming, TTL strategy, and serialization config.

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Configure a Rails project to work with Conductor (parallel coding agents)

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Configura cobertura de tests y CI pipeline

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One-time setup that gathers design context for your project and saves it to your AI config file. Run once to establish persistent design guidelines.

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Migrate supported instruction files, skills, agents, and MCP config into Codex project and global files.

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Optimize Bazel builds for large-scale monorepos. Use when configuring Bazel, implementing remote execution, or optimizing build performance for enterprise codebases.

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Azure Bot Service Management SDK for Python. Use for creating, managing, and configuring Azure Bot Service resources.

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