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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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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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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

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集群数据管理 Skill —— 涵盖数据使用规范、压缩优化、数据共享（ACL）、文件扫描与清理、文件完整性校验、genozip 基因组压缩等全流程。Use when the user asks about: managing data on the HPC cluster, compressing genomic files (fq/bam/vcf), sharing data between users/groups, scanning for large files or cleaning up disk space, checking file integrity (md5/gzip/bam), using genozip, checking disk quota, or any data lifecycle management task on the NCPGR HPC cluster.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.

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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

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Spring Boot architecture patterns, REST API design, layered services, data access, caching, async processing, and logging. Use for Java Spring Boot backend work.

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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 expert knowledge of JPA entity design, relationship mapping, Flyway migrations, and PostgreSQL-specific optimizations.

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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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Provides patterns for implementing Spring Boot caching: configures Redis/Caffeine/EhCache providers with TTL and eviction policies, applies @Cacheable/@CacheEvict/@CachePut annotations, validates cache hit/miss behavior, and exposes metrics via Actuator. Use when adding caching to Spring Boot services, configuring cache expiration, evicting stale data, or diagnosing cache misses.

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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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Verifies and injects Google Tag Manager (GTM), GA4 event triggers, and optimized meta tags.

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Use when integrating LLMs, chat clients, embeddings, RAG pipelines, or AI agents into Spring Boot. Covers Spring AI ChatClient, prompt templates, embeddings, vector stores, and structured output. Use when user mentions Spring AI, LLM, ChatGPT, Claude, RAG, embeddings.

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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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Generates strictly typed Drizzle ORM schemas for PostgreSQL with indexes, foreign keys, and Zod schema deduction.

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Use when creating database migrations, schema changes, seed data, or any SQL that modifies database structure. Covers Flyway naming conventions, versioning, and safe migration patterns.

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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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Inventory staged local EcoSIM data at project startup and validate input readiness for a selected site, simulation period, and preprocessing or analysis workflow. Use before data-dependent work or when relevant inputs change.

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Plans Convex schema and data migrations with widen-migrate-narrow and @convex-dev/migrations. Use for breaking schema changes, backfills, table reshaping, or zero-downtime rollouts.

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