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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.

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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.

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Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling, and LD-aware regional rendering. Use when visualizing association results across the genome, comparing two traits, computing genomic inflation lambda, or zooming into a locus with LD coloring.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.

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Generate, fill, and assemble PDF documents at scale. Handles legal forms, contracts, invoices, certificates. Supports form filling (pdf-lib), template rendering (Puppeteer, LaTeX), digital signatures (DocuSign), and document assembly. Use for legal tech, HR automation, invoice generation. Activate on "PDF generation", "form filling", "document automation", "digital signatures". NOT for simple PDF viewing, basic file conversion, or OCR text extraction.

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Runs an iterative, conversational product-discovery process with a founder/stakeholder: structured interview, live low-fi wireframing, a linked feature/page node-graph built up as you go, a founder-confirmed lock-in checkpoint, then a generated PRD, a Mermaid-rendered sitemap, and a mockup with a full design system (palette, typography, dark mode). Use when building or operating an AI product-discovery chatbot, or when running founder/stakeholder discovery by hand and you need the structure (interview script, node-graph schema, PRD template, design-system handoff order). NOT for implementing the spec'd product once locked — hand off to feature-specific skills (ideal-web-app-builder, tailwind-v4-expert, color-theory-palette-harmony-expert, typography-expert, dark-mode-design-expert) for that. NOT for one-shot PRD generation without an interview loop — if the founder already has a written spec, this process is unnecessary overhead.

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Own whether a multi-document product-architecture binder is internally consistent, complete against its stated customer/contingency/architecture coverage, and honest about which older product ambitions it has absorbed, superseded, deferred, contradicted, orphaned, or rejected. Use when running a binder Architect of Record pass, before an implementation chain cites a binder chapter as ready, when a proof-gate owner is missing, or when reconciling the binder against the older ambition corpus (website, plans, examples, ADRs). NOT for auditing a single Claude Skill bundle's structure or frontmatter (use skill-hygiene), rendering a single-PM accept/reject verdict on one finished deliverable (use port-daddy-user-surrogate-pm-review), or sequencing/stewarding a roadmap's sidequests once a gap or operator decision has been surfaced (use legible-roadmap-with-sidequests).

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Design performant animation systems with Framer Motion, GSAP, View Transitions API, and spring physics. Activate on: page transitions, micro-interactions, scroll animations, layout animations, spring physics. NOT for: CSS-only hover effects (use css-in-js-architect), video/canvas rendering (use creative-coding-expert).

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Expert-level idiomatic Rust API design — the patterns that make illegal states unrepresentable and abstractions zero-cost. Type-state programming (PhantomData state machines), newtype + sealed + extension traits, typestate builders, RAII guards & Drop ordering, the interior-mutability decision tree (Cell/RefCell/Mutex/RwLock/Atomic/OnceLock), enum-driven state machines, error architecture (thiserror vs anyhow), dyn vs generic dispatch & object safety, the impl Trait / GAT / RPITIT toolbox, and Deref-for-smart-pointers (and its abuse). Use when designing a Rust library's public API, encoding invariants in the type system, choosing a dispatch or error strategy, or reviewing Rust for idiom. NOT for borrow-checker firefighting / toolchain / test-runner workflow (use rust-development-workflow), NOT for pd-console GPUI rendering/layout/panes (use gpui-rust-console), NOT for app packaging/notarization (use rust-app-distribution).

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Technical SEO audit across 9 categories: crawlability, indexability, security, URL structure, mobile, Core Web Vitals, structured data, JavaScript rendering, and IndexNow protocol. Use when user says "technical SEO", "crawl issues", "robots.txt", "Core Web Vitals", "site speed", or "security headers".

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Full-site crawling, scraping, and site mapping via Firecrawl MCP. Use when user says "crawl site", "map site", "full crawl", "find all pages", "broken links", "site structure", "discover pages", "JS rendering", or needs site-wide analysis.

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WindowPanel (@ai-matrx/summon/window) and its window manager. Use when a window won't drag, resize, minimize or pop out, the tray or restore is wrong, rendering <WindowPanel> on a page, or editing features/window-panels/**. NOT for opening or registering overlays (use overlay-system).

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Collapsing every copy of one kind of thing (tables, UIs, hooks, APIs, renderers) into a single canonical one. Use when asked to unify, merge, converge, or 'make one X used everywhere', before migrating callers onto a new canonical piece, or removing a duplicate component. NOT for docs (use docs).

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The Shape System — the content_ir kind registry for structured content. Use when adding, activating, or rendering a kind/shape, writing `__kind` JSON, kind schemas or samples, XML-tag/fence detection surfaces, kind components, workflow node input_kind/output_kind, or binding agent output to a kind.

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Rules for every string rendered inside the app, plus the sweep that removes in-app prose. Use when writing or changing a label, hint, description, tooltip, empty state or KPI tile in a .tsx file, or when running Pattern Patrol P14 or asked to find or fix long UI text.

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The staged pipeline that turns any API, provider payload, scrape, or computed result into registered, rendered platform kinds. Use on 'create kinds for X', 'distill X into kinds', 'point yourself at API X', or as a stage (A/B/V/D/C) of a running data-to-kinds run. NOT for consuming existing kinds (use aidream's workflow-io-kinds / matrx-frontend's shape-system).

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Printing and PDF export for AI response blocks and messages via @ai-matrx/print. Use when adding a print button or BlockPrinter to a render block, wiring PrintOptionsDialog/usePrintOptions, captureBlockElement, or useDomCapturePrint, or when a print window shows no images or a print fails silently.

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Export a Remotion video

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React composition patterns that scale. Use when refactoring components with boolean prop proliferation, building flexible component libraries, or designing reusable APIs. Triggers on tasks involving compound components, render props, context providers, or component architecture. Includes React 19 API changes.

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Three.js geometry creation - built-in shapes, BufferGeometry, custom geometry, instancing. Use when creating 3D shapes, working with vertices, building custom meshes, or optimizing with instanced rendering.

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Comprehensive guide for developing WebGPU-enabled Three.js applications using TSL (Three.js Shading Language). Covers WebGPU renderer setup, node materials, compute shaders, post-processing, and WGSL integration. Use when working with Three.js WebGPU, TSL shaders, or GPU compute pipelines.

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Best practices for Remotion video creation in React. Use when building, reviewing, or optimizing Remotion compositions, animation timing, assets, captions, and render pipelines.

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Builds simple Three.js web apps with scene setup, lighting, geometry, materials, animation, and responsive rendering. Use when creating or prototyping 3D web scenes with modern Three.js (r150+).

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