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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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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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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers between conditions, identifying master transcription factor networks, or predicting BET-inhibitor responsiveness.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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Use when implementing or debugging ANY network connection, API call, or socket in an Apple app. Covers URLSession, Network.framework, NetworkConnection, connection diagnostics.

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Build, review, or improve networking code in iOS/macOS apps using URLSession with async/await, structured concurrency, and modern Swift patterns. Use when working with REST APIs, downloading files, uploading data, WebSocket connections, pagination, retry logic, request middleware, caching, background transfers, or network reachability monitoring. Also use when handling HTTP requests, API clients, network error handling, or data fetching in Swift apps.

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This skill should be used when creating Ultralytics-branded content of any kind, including PDF, PPTX, Canva, or Google Slides presentations, DOCX documents, marketing or newsletter HTML emails, social media post copy or visuals, website or landing page designs, and dataset or model result visuals. Provides official colors, typography, logo rules, naming rules, and tone of voice from ultralytics.com/brand.

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Simulate Bluetooth system-level networks using the Bluetooth Toolbox. Use this skill for any Bluetooth topology: BLE ACL (Asynchronous Connection-Less) data connections, CIS (Connected Isochronous Stream) and LE Audio for stereo speakers or hearing aids, BLE GAP (Generic Access Profile) connection establishment with advertising and scanning, Classic BR/EDR piconets with ACL data and SCO (Synchronous Connection-Oriented) voice links, and BLE+BR/EDR coexistence with adaptive frequency hopping. Covers bluetoothLENode, bluetoothNode, bluetoothLEConnectionConfig, bluetoothLECISConfig, bluetoothLEGAPConfig, bluetoothConnectionConfig, configureConnection, kpi (), updateChannelList, and all Bluetooth statistics.

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Use when setting up vehicle network communication in MATLAB using Vehicle Network Toolbox. Covers CAN/CAN FD (fully implemented), with architecture for J1939, XCP, and future protocols. Handles hardware discovery, channel creation, bus configuration, message exchange, signal encoding/decoding, and analysis across all supported vendors. (Vector, Kvaser, PEAK-System, NI, SocketCAN, MathWorks Virtual).

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AWS Cognito user authentication and authorization service. Use when setting up user pools, configuring identity pools, implementing OAuth flows, managing user attributes, or integrating with social identity providers.

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Shopify/DTC brand protection toolkit. Detect counterfeit stores, unauthorized resellers, and trademark violations. Includes DMCA takedown templates, domain monitoring, and social media infringement detection. No API key required.

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Review strategy for TikTok Shop — encouraging reviews, responding, leveraging UGC, social proof

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Full-stack e-commerce marketing strategy builder. Analyzes your product, market, and competitors, then builds a complete omnichannel marketing plan covering paid ads, SEO, email/SMS, content marketing, social media, influencer partnerships, and referral programs. Includes target audience persona, competitive landscape, channel prioritization with budget allocation, content direction, and a 90-day action plan. Works for any e-commerce platform — Shopify, Amazon, Etsy, WooCommerce, TikTok Shop, and more. No API key required.

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Brand monitoring tool for tracking mentions across social media platforms. Monitor Reddit, Google News, YouTube, and DuckDuckGo for brand mentions. Includes sentiment analysis, trend tracking, crisis detection, and competitor comparison. No API key required for basic monitoring.

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Use when the operator wants a hero or meta image for a Prisma blog post; asks to create or generate a blog hero, cover, social card, Open Graph, or YouTube image; mentions cover art, a blog thumbnail, cover.svg/hero.svg/meta.png; references content-create-hero-image; or wants to interactively design cover imagery in Prisma's 2026 brand (light paper, prism accents, Sora). Produces an editable SVG hero plus a pixel-exact PNG meta image, and includes an interactive mode and a built-in design-review pass.

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24/7 autonomous business operations orchestrator with business health scoring, canary monitoring, and safety guardrails. Schedules and runs all business functions automatically — content publishing, social media posting, outreach sequences, ad monitoring, financial reporting, health checks, and post-deploy verification. Use when the user wants to automate operations, schedule tasks, set up autonomous workflows, or says 'automate this', '24/7', 'run automatically', 'schedule', 'cron', 'autonomous', or 'set and forget'.

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Automated content creation pipeline for business growth. Creates blog posts, landing pages, email sequences, social media content, and video scripts with a supply-demand topic gate, 5-dimensional quality diagnosis, one-core resonance check, per-sentence information density scoring, 12-signal authenticity audit, headline impact matrix, content substance scoring, and a cheap-format MVP testing ladder. Use when the user needs content marketing, blog posts, email sequences, copywriting, video scripts, or says 'write content', 'blog post', 'email sequence', 'content calendar', 'marketing copy', 'video script', or 'hook'.

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Deep business diagnosis for when things aren't working. Uses Socratic questioning, first-principles reasoning, and constraint analysis to find WHY a business is stuck — not just prescribe solutions. Use when the user says 'my business isn't working', 'I'm stuck', 'what's wrong', 'diagnose my business', 'why am I not growing', 'help me figure out the problem', or describes a specific business challenge.

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Debug production-like issues in this repository with disciplined evidence gathering. Use when fixing failing workflows, regressions, flaky behavior, or data inconsistencies across hooks, API, DB, websocket, and UI.

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MANDATORY for every coding agent (Claude Code, Codex, or any other) — keep this repository's documentation in sync after any change to behavior, configuration, interfaces, events, schema, or features. Use automatically at the end of change-sets that alter an env var, event type, hook or state behavior, API, schema, WebSocket message, MCP tool, CLI command, or user-facing feature, and whenever the user asks to update documentation.

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。