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Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and which transcription factors control them?" by layering expression, chromatin accessibility, histone marks, and TF binding data. Follows the Mawla et al. 2023 framework for cross-assay integration of islet cell type-specific data. Handles chromatin state annotation (ChromHMM), enhancer-gene linkage, TF motif enrichment, and cell type-specific regulatory element identification. Use for ANY multi-omic analysis, enhancer discovery, regulatory network construction, or epigenomic characterization using ENCODE data.

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Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.

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Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods, generate figure legends, create supplementary tables, draft data availability statements, compile tool citations, or auto-generate any publication text from their ENCODE analysis. Trigger on: methods section, figure legend, supplementary table, data availability, tool citations, publication writing, manuscript, write methods, methods draft, write up, write-up, paper writing, reproducible methods.

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Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif database, binding profile, PWM, position weight matrix, TF motif, motif enrichment, motif scanning, binding site prediction.

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Creates feature branches with optimized short naming, auto-incrementing, and commit type detection (feat/fix/refactor). Supports manual descriptions and auto-generation from uncommitted git changes. Use when user requests to create branch, start new branch, make branch, checkout new branch, switch branch, new task, start working on, begin work on feature, begin feature, create feature branch, run /create-branch command, or mentions "branch", "feature", "new feature", "feat", "fix", or "checkout".

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Scan a project to detect configured quality and testing tools across JVM (Gradle/Maven), Android (AGP/Compose/KMP), Node.js/TypeScript, and Python ecosystems. Cross-reference against research-backed recommendations and assist with setup. Auto-detects project type(s) including monorepos with mixed ecosystems. Use when user asks to "audit tooling", "recommend tools", "quality stack", "what tools am I missing", "setup eslint", "setup detekt", "add coverage", "add ruff", "configure CI quality pipeline", "scan project tools", "tooling audit", "android tooling", "android quality", "compose testing", "kmp testing", or "screenshot testing".

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Creates isolated git worktrees in .claude/worktrees/ with intelligent branch naming, auto-incrementing, and commit type detection (feat/fix/refactor). Supports manual descriptions and auto-generation from uncommitted git changes. Use when user requests to create worktree, start isolated work, parallel development, run /worktree command, or mentions "worktree".

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Converts natural-language descriptions or UI spec files into optimized Google Stitch prompts. Use when creating, refining, or validating design directives for Google Stitch. Use when user says "create a Stitch prompt", "optimize this for Stitch", "convert this spec to a Stitch prompt", "write a UI prompt", or mentions Google Stitch prompt authoring. Follows Stitch best practices with short, directive prompts focused on screens, structure, and visual hierarchy.

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Technical SEO audit across 8 categories: crawlability, indexability, security, URL structure, mobile, Core Web Vitals, structured data, and JavaScript rendering. Enhanced with live GSC (indexing status, crawl data) and Ahrefs (backlink profile) data when MCPs are available. Use when user says "technical SEO", "crawl issues", "robots.txt", "Core Web Vitals", "site speed", or "security headers".

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Audit markdown files for SEO before publishing. Checks heading structure, meta description, keyword density, content length, link quality, image alt text, and frontmatter completeness. Use when user says "markdown audit", "check my markdown", "SEO check markdown", or "audit this post".

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Analyze internal link structure by crawling a domain. Identifies orphan pages, underlinked pages (configurable heuristic, default fewer than 3 inbound links), and broken internal links. Suggests anchor text for top 5 underlinked pages. Reuses existing fetch/parse scripts. Optional Ahrefs enrichment. Use when user says "internal links", "link structure", "orphan pages", "internal linking", "link graph", "anchor text audit".

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Use this when the user wants to generate, normalize, verify, deduplicate, or export training datasets for Codex, Antigravity, or Claude Code from topics, URLs, reference material, web research, or existing JSONL/CSV files. Supports SFT and DPO workflows, custom export schemas, and deterministic local pipeline scripts.

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Drive running Unity Editor from shell to verify compiles, playmode, scenes, screenshots. Use when editing C# scripts, scenes, or assets in a Unity project and needing to: (1) check compilation succeeds, (2) read console errors, (3) enter/exit Play mode, (4) capture screenshots or frame recordings, (5) select objects or aim the Scene camera, (6) query editor window layout. Injects a file-polling command bridge (UnityRemote.cs) — prefer this over batchmode (fights the Library lock) or GUI automation.

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Use this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants to: open, read, edit, or fix an existing .xlsx, .xlsm, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting, charting, cleaning messy data); create a new spreadsheet from scratch or from other data sources; or convert between tabular file formats. Trigger especially when the user references a spreadsheet file by name or path — even casually (like "the xlsx in my downloads") — and wants something done to it or produced from it. Also trigger for cleaning or restructuring messy tabular data files (malformed rows, misplaced headers, junk data) into proper spreadsheets. The deliverable must be a spreadsheet file. Do NOT trigger when the primary deliverable is a Word document, HTML report, standalone Python script, database pipeline, or Google Sheets API integration, even if tabular data is involved.

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Language-specific guidelines for producing high-quality Traditional Chinese (zh-TW) content: script, full-width punctuation, spacing, forms of address, grammar constraints, and Taiwan terminology. Includes the no-calque rule against literal translations of English phrasal verbs such as 折入 for fold in. Use when writing any kind of Chinese content. Including blog posts, notes, technical articles, technical writing, chitchat, social media posts, etc., even when you are just sending a text message. Also use when reviewing or editing existing Chinese content for language and terminology compliance. Always apply `writing-style-guideline` alongside this skill for structure, tone, rhetorical constraints, and banned phrases.

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Create and refine CS paper main figures, framework diagrams, case illustrations, and quantitative charts from manuscripts and real data, with self-explanatory labels and final-size PDF checks.

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Write engaging PR titles and descriptions for any forge (GitHub today; Bitbucket planned). Use when creating or updating PRs. Leads with narrative paragraphs and reaches for lists, tables, and diagrams when content is genuinely structured.

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Generate a PR_MESSAGE.md file from session context using GitHub CLI. Detects related issues via branch-keyword search, writes a structured PR description with commit subject, summary, test plan, and changelog. Validates with commitlint and markdownlint. Use when preparing a pull request on GitHub.

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Create pull requests with structured description

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Use when building CLI tools, implementing argument parsing, or adding interactive prompts. Invoke for parsing flags and subcommands, displaying progress bars and spinners, generating bash/zsh/fish completion scripts, CLI design, shell completions, and cross-platform terminal applications using commander, click, typer, or cobra.

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Detect project linting and validation tools, build an execution pipeline, run all tools to zero errors, and fix issues using an atomic fix protocol. Auto-detects Makefile targets, package.json scripts, Go tools, Python tools, and other common linters. Use when fixing linting errors, running validation pipelines, or ensuring code quality before committing.

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Defines service level objectives, creates error budget policies, designs incident response procedures, develops capacity models, and produces monitoring configurations and automation scripts for production systems. Use when defining SLIs/SLOs, managing error budgets, building reliable systems at scale, incident management, chaos engineering, toil reduction, or capacity planning.

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Create or update the feature specification from a natural language feature description.

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Xilinx/AMD Vivado FPGA build workflow -- batch-mode TCL scripting, ADI HDL reference design integration, Zynq-7000/MPSoC block design, IP builds, synthesis, implementation, and bitstream generation. Use for any Zynq or UltraScale+ design that incorporates ADI transceivers or follows the ADI HDL reference design pattern.

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