264 件 ・ 関連度順
概要と使いどころ
Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, genome-wide association, SNP association, trait association, GWAS Catalog, disease association, risk variant, lead SNP, LD proxy.
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Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.
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Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with confidence annotations. Handles cross-lab batch effects, broad vs narrow marks, and ENCODE blocklist filtering.
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Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact on regulatory elements, perform enrichment testing of variant sets in tissue-specific annotations, or link variants to target genes through enhancer-gene maps. Handles the full post-GWAS workflow from variant set → tissue mapping → functional annotation → fine-mapping awareness → enrichment → variant-to-gene → prioritization. Use this skill for ANY variant interpretation task involving ENCODE chromatin, accessibility, TF binding, or 3D genome data.
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Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene constraint (pLI, LOEUF) for ENCODE target genes, needs population-specific frequencies for GWAS variants overlapping cCREs, wants to filter variants by rarity before functional annotation, or is interpreting ENCODE CRISPR/MPRA results in the context of population genetics. Also use when the user mentions gnomAD, allele frequency, pLI, LOEUF, constraint, rare variants, population frequency, ExAC, or variant filtering.
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Smart code scanner that detects Spring Boot patterns and routes to appropriate skills. Use when editing Java or Kotlin files in Spring Boot projects, working with pom.xml/build.gradle containing spring-boot-starter, or when context suggests Spring Boot development. Detects annotations (@RestController, @Entity, @EnableWebSecurity, @SpringBootTest) to determine relevant skills and provides contextual guidance. Uses progressive automation - auto-invokes for low-risk patterns (web-api, data, DDD), confirms before loading high-risk skills (security, testing, verify).
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Documenting As-Is and To-Be business processes for a Salesforce project as swim-lane diagrams — one lane per actor, explicit decision points, parallel and exception/sad paths, and per-step automation-tier annotations that drive downstream build decisions. Trigger keywords: As-Is To-Be salesforce process, swim lane salesforce, business process map, automation candidate identification, sad path documentation, process actor mapping, manual residue. NOT for Opportunity stage and exit-criteria design — use admin/sales-process-mapping. NOT for picking Flow vs Apex for one requirement — use admin/process-automation-selection.
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Remove AI-generated code smells (slop) from branch changes or an explicit file list. Locks behavior with regression tests FIRST, then runs categorized cleanup via parallel `deep` agents in batches of 5, then verifies with quality gates. Covers 10 slop categories including performance equivalences, excessive complexity (object annotations, if/elif variant chains), and oversized modules (250+ pure LOC with mandatory modular refactoring). MUST USE when the user asks to "remove slop", "clean AI code", "deslop", "clean up AI-generated code", "remove AI slop", or wants to clean up AI-generated patterns from recent changes. Triggers - "remove ai slops", "clean ai code", "deslop", "cleanup AI generated", "remove AI slop", "clean up AI-generated code", "strip slop", "ai-slop cleanup".
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Use when writing Playwright tests, fixing flaky tests, debugging failures, implementing Page Object Model, configuring CI/CD, optimizing performance, mocking APIs, handling authentication or OAuth, testing accessibility (axe-core), file uploads/downloads, date/time mocking, WebSockets, geolocation, permissions, multi-tab/popup flows, mobile/responsive layouts, touch gestures, GraphQL, error handling, offline mode, multi-user collaboration, third-party services (payments, email verification), console error monitoring, global setup/teardown, test annotations (skip, fixme, slow), test tags (@smoke, @fast, @critical, filtering with --grep), project dependencies, security testing (XSS, CSRF, auth), performance budgets (Web Vitals, Lighthouse), iframes, component testing, canvas/WebGL, service workers/PWA, test coverage, i18n/localization, Electron apps, or browser extension testing. Covers E2E, component, API, visual, accessibility, security, Electron, and extension testing.
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Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reassembly + PairHMM mechanism (why HC beats pileup callers on indels), the -ERC GVCF reference-confidence model and <NON_REF> allele, BQSR-vs-DRAGSTR and --dragen-mode error modeling, allele-specific (AS_) annotations, and edge cases (ploidy, Mutect2 mitochondria mode, sex chromosomes/PAR, contamination gating). Use when deciding whether to use HaplotypeCaller vs a pileup or DRAGEN caller, whether BQSR still earns its place, whether to call per-sample GVCFs for a cohort, or how to handle non-diploid, mitochondrial, sex-chromosome, or contaminated samples. Not for post-calling filtering depth (see variant-calling/filtering-best-practices) or cohort joint-genotyping scaling (see variant-calling/joint-calling).
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Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO. Use when changing a file format for a downstream tool, fixing FASTQ quality encoding (Phred+33 vs Phred+64 vs Solexa), or when a conversion risks silently dropping annotations or quality scores.
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Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.
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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.
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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.
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Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.
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。
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.
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。
Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.
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Generate hand-drawn style diagrams and infographics for recovery education articles. Creates anatomist's notebook aesthetic visuals - brain diagrams, timelines, social comparisons, and process flows using continuous line art, semantic color coding, and margin annotations.
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Use when creating a new Laravel API endpoint — Controller, FormRequest, Resource, route, Policy, OpenAPI annotations — versioned route layout, single-action `__invoke` controllers.
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。
Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.
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。
Recast a supplied everyday photo as a witty illustrated product instruction sheet with a large Chinese title and concise English annotations. Use for 日常说明书、宠物使用说明、生活物品冷幽默说明图 or a fictional everyday object manual poster.
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Register WordPress Abilities: machine-readable plugin operations with JSON Schema contracts, required permission callbacks, optional REST exposure, and AI/MCP-friendly discovery. Covers categories, wp_register_ability, WP_Ability::execute, REST run endpoints, meta.show_in_rest, annotations, and Ability vs REST route vs custom hook decisions. Use when exposing plugin functionality to agents, admin JS, external tools, or reviewing AI integration code.
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Bootstrap an AI-agent skill from a TypeScript codebase by running the deterministic skillit generate/audit loop and enriching repo source (JSDoc, README, config-type properties, MCP tool annotations, examples, package.json) until the skill reaches its grade target. Use for cli, typedoc, config, or mcp (build-mode) projects; never edit SKILL.md/references directly.
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MCP server documentation conventions for high-quality generated skills. Use when writing tool descriptions, `_meta` annotations, or input schemas for MCP extraction.
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。