「cti」の検索結果

View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

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。

Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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。

Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

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。

Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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。

Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

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The CI cost rules ($100/week of real money, all CI). Use when editing .github/workflows, adding a schedule or cron, dispatching a workflow, publishing a package version, hitting a billing block, or seeing a CI SPEND OFF TRACK line, ci-breaker issue or spend alert.

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Spring Security best practices for authn/authz, validation, CSRF, secrets, headers, rate limiting, and dependency security in Java Spring Boot services.

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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 REST API design standards and best practices for Spring Boot projects. Use when creating or reviewing REST endpoints, DTOs, error handling, pagination, security headers, HATEOAS and architecture patterns.

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Provides fault tolerance patterns for Spring Boot 3.x using Resilience4j. Use when implementing circuit breakers, handling service failures, adding retry logic with exponential backoff, configuring rate limiters, or protecting services from cascading failures. Generates circuit breaker, retry, rate limiter, bulkhead, time limiter, and fallback implementations. Validates resilience configurations through Actuator endpoints.

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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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Provides integration patterns for LangChain4j with Spring Boot. Configures AI model beans, sets up chat memory with Spring context, integrates RAG pipelines with Spring Data, and handles auto-configuration, dependency injection, and Spring ecosystem integration. Use when embedding LangChain4j into Spring Boot applications, building Java LLM applications with @Bean configuration, or setting up Spring AI patterns.

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Build production Spring Boot applications - REST APIs, Security, Data, Actuator

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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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Kotlin/Spring Boot 3.x patterns - use for backend services, REST APIs, dependency injection, controllers, and service layers

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JPA/Hibernate patterns for entity design, relationships, query optimization, transactions, auditing, indexing, pagination, and pooling in Spring Boot.

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Provides a structured framework for conducting thorough code reviews covering correctness, security, architecture alignment, performance, and technical debt.

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Use when building MCP (Model Context Protocol) servers in Java/Spring Boot. Covers tool registration, resource exposure, prompt templates, and production deployment using the official MCP Java SDK. Use when user mentions MCP, AI agent integration, or tool calling.

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Use when generating JPA entities, repositories, queries, or anything touching the persistence layer. Covers entity conventions, N+1 prevention, projections, and query patterns.

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Use when adding hypermedia links to REST responses, building self-describing APIs, or implementing Spring HATEOAS. Use when you see EntityModel, CollectionModel, or RepresentationModel in the project.

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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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Picks the model a coding agent uses when a test or browser check sends an AI call. Use when choosing a model for any test, UI check, bench, or agent run, or when a test names Opus, Sonnet, Fable, Astra, or any model by habit.

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。