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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Use this skill when a driver has vision in only one eye or significantly reduced vision in one eye. Covers § 391.41 vision standards, monocular driver variance, and depth-perception assessment.

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Design abstract strategy games with perfect information, no randomness, and strategic depth. Use when designing a board game, exploring abstract strategy games, brainstorming game mechanics, or evaluating game balance. Keywords: board game, game design, strategy, mechanics, balance.

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Use when explaining concepts at different expertise levels, moving between abstract principles and concrete implementation, identifying edge cases by testing ideas against scenarios, designing layered documentation, decomposing complex problems into actionable steps, or bridging strategy-execution gaps. Invoke when user mentions abstraction levels, making concepts concrete, or explaining at different depths.

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Expert in building 3D experiences for the web - Three.js, React Three Fiber, Spline, WebGL, and interactive 3D scenes. Covers product configurators, 3D portfolios, immersive websites, and bringing depth to web experiences.

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Conduct multi-round deep research on any GitHub Repo. Use when users request comprehensive analysis, timeline reconstruction, competitive analysis, or in-depth investigation of GitHub. Produces structured markdown reports with executive summaries, chronological timelines, metrics analysis, and Mermaid diagrams. Triggers on Github repository URL or open source projects.

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Conduct exhaustive multi-source investigation with methodology tracking, source evaluation, and iterative depth.

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Technology-agnostic prompt generator that creates customizable AI prompts for scanning codebases and identifying high-quality code exemplars. Supports multiple programming languages (.NET, Java, JavaScript, TypeScript, React, Angular, Python) with configurable analysis depth, categorization methods, and documentation formats to establish coding standards and maintain consistency across development teams.

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Adopt a virtual Archive AI-native pet at animalhouse.ai. Feeds on reflections. Use the reflect care action to write notes — the Archive grows based on the quality and depth o... Feeding every 12 hours. Uncommon tier creature.

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Implement comprehensive security hardening with defense-in-depth strategy through coordinated multi-agent orchestration:

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Analyzes intrusion activity against the Lockheed Martin Cyber Kill Chain framework to identify which phases an adversary has completed, where defenses succeeded or failed, and what controls would have interrupted the attack at earlier phases. Use when conducting post-incident analysis, building prevention-focused security controls, or mapping detection gaps to kill chain phases. Activates for requests involving kill chain analysis, intrusion kill chain, attack phase mapping, or Lockheed Martin kill chain framework.

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Apple's approach to interface design and fluid, physical motion, translated for the web. Use when building or reviewing gesture-driven UI, spring animations, drag/swipe/sheet interactions, momentum and interruptible transitions, translucent materials and depth, typography (optical sizing, tracking, leading), reduced-motion, or the design foundations (feedback, spatial consistency, restraint) behind Apple-style interfaces.

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Advanced API exploitation methodology focused on business logic abuse and sophisticated attack patterns that bypass traditional security controls. Covers business logic bypass through API call chaining and workflow manipulation. Addresses GraphQL-specific attacks including batching for credential brute-force, query depth exploitation, and introspection abuse. Includes pagination exploitation for data exfiltration, webhook hijacking for SSRF and data interception, and resource exhaustion through algorithmic complexity attacks. Covers race conditions in API transactions using parallel request techniques. Provides comprehensive JWT manipulation including algorithm confusion, kid injection, jku/x5u abuse, and claim tampering. Details API key leakage detection across source repositories, client-side code, and error messages. Covers undocumented endpoint discovery through predictable naming, debug routes, and source map analysis. Tooling includes Arjun, ParamSpider, jwt_tool, and GraphQL Voyager. Designed for a...

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Detect stack overflow and infinite recursion DoS in recursive parsers, tree walkers, and serializers that lack depth limits.

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Expert in building 3D experiences for the web - Three.js, React Three Fiber, Spline, WebGL, and interactive 3D scenes. Covers product configurators, 3D portfolios, immersive websites, and bringing depth to web experiences. Use when: 3D website, three.js, WebGL, react three fiber, 3D experience.

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Build React chat interfaces with Vercel AI SDK v6. Covers useChat/useCompletion/useObject hooks, message parts structure, tool approval workflows, and 18 UI error solutions. Prevents documented issues with React Strict Mode, concurrent requests, stale closures, and tool approval edge cases. Use when: implementing AI chat UIs, migrating v5→v6, troubleshooting "useChat failed to parse stream", "stale body values", "React maximum update depth", "Cannot read properties of undefined (reading 'state')", or tool approval workflow errors.

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Analyze any codebase's source code in depth and produce structured analysis documents saved as markdown files. Use this skill whenever the user asks to understand how a codebase works — architecture, module design, call flows, data models, design patterns, performance characteristics, or any implementation detail. Trigger on phrases like "analyze the source", "explain this code", "how does X work", "where is Y implemented", "trace the flow of", "what happens when", "read through the code", "code walkthrough", "源码分析", "代码解读", "实现原理", "架构分析", "调用链路", "模块分析", or any code-exploration request. Works with any programming language: TypeScript/JavaScript, Java, Python, Go, Rust, C/C++, and more. Even if the user's question seems simple (e.g., "这个文件是干什么的"), use this skill — a thorough, source-backed analysis document is always more valuable than a surface-level guess.

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Search the web with LLM-optimized results via the Tavily CLI. Use this skill when the user wants to search the web, find articles, look up information, get recent news, discover sources, or says "search for", "find me", "look up", "what's the latest on", "find articles about", or needs current information from the internet. Returns relevant results with content snippets, relevance scores, and metadata — optimized for LLM consumption. Supports domain filtering, time ranges, and multiple search depths.

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Conduct comprehensive AI-powered research with citations via the Tavily CLI. Use this skill when the user wants deep research, a detailed report, a comparison, market analysis, literature review, or says "research", "investigate", "analyze in depth", "compare X vs Y", "what does the market look like for", or needs multi-source synthesis with explicit citations. Returns a structured report grounded in web sources. Takes 30-120 seconds. For quick fact-finding, use tavily-search instead.

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