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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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。

Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular per-region CNN with calibrated ΔPSI), SpliceTransformer/TrASPr (tissue-aware transformers), SpliceVault (empirical 300K-RNA lookup of likely mis-splicing outcomes), CADD-Splice (composite score). Applies the ClinGen SVI 2023 framework for ACMG/AMP variant interpretation (PVS1, PP3, BP4 evidence codes), HGVS splicing nomenclature (c.123+1G>A, c.123-3T>G, r.spl?), extended-window scoring for deep-intronic pseudoexons, tissue-specific predictions, branchpoint variant detection (BPHunter, LaBranchoR), and splice-switching ASO design. Use when interpreting splice impact of clinical variants, prioritizing VUS, identifying deep-intronic pathogenic variants, or designing ASOs.

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。

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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。

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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 alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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。

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

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。

Bing Webmaster Tools + IndexNow extension. Microsoft Copilot citations are fed by the Bing index; this skill makes Bing visibility, link data, and IndexNow URL submission first-class.

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。

Recipe for creating or changing a floating window panel. Use when adding a window, editing a window component, adding persistence, onCollectData, or ephemeral mode, wiring the Tools grid, or a window fails to restore after reload. NOT for WindowPanel drag/resize/tray internals (use window-panels).

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One-route pattern: public marketing landing plus signed-in workspace. Use when creating or fixing a landing page or a feature's front door, guests see an error, 'make /X work signed out', signed-in users land on a pitch, or ModuleLanding / AuthedWorkspaceCTA. NOT for (public) share viewers or free tools.

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。

Pre-ship safety proof for replacing a live implementation with a canonical one. Use when repointing nodes, tools, or services to a new contract, superseding a schema, retiring a legacy or parallel system, or any 'new way replaces the old way' change. NOT for greenfield or unconsumed additive work.

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。

Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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This skill should be used when the user asks to "ドキュメントを更新して", "sync the docs", "update CLAUDE.md after this change", "実装に合わせてドキュメントを直して", or notices that docs have drifted from the codebase. Diffs git history to identify what changed, proposes targeted updates to CLAUDE.md, docs/architecture.md, docs/requirements.md, and README.md, then applies only approved changes.

サブエージェントを活用した並列実行・調査委譲・コンテキスト管理の戦略。複雑な問題への対処、調査・探索タスク、複数の選択肢の比較検討、大規模なリファクタリングなどでこのスキルを参照する。「調べて」「比較して」「並列で」「複数のアプローチを試して」といったリクエストや、メインのコンテキストが肥大化しそうな場面で使う。

This skill should be used when the user asks to "このファイルを変えたら何が壊れる？", "what depends on this function", "影響範囲を調べて", "show me what imports this module", or wants to understand the blast radius before modifying a shared utility, exported type, or public API. Traces import/require references up to two levels deep and lists affected test files.

This skill should be used when the user asks to "PR を出す前に確認して", "check if this branch is ready to merge", "run pre-PR checks", "PRを作る前にチェックして", or wants to verify a branch before opening a pull request. Executes verification commands, validates Conventional Commits format, and confirms documentation is updated, then reports whether gh pr create is safe to run.

This skill should be used when the user asks to "既存プロジェクトのタスクを整理して", "技術的負債をIssue化して", "このコードベースを改善するタスクを洗い出して", "GitHub Projectに健全化タスクを登録して", "break down what needs to be fixed in this project", "surface tech debt as issues", or "create a project board for cleanup work". Diagnoses pain points and codebase health of an existing project, then registers improvement tasks as GitHub Issues and a Project Board.

This skill should be used when the user asks to "このエラーを直して", "help me debug this", "fix this stack trace", "なぜこのエラーが出るの", "CI が落ちた", or pastes an error message or stack trace and wants help diagnosing it. Classifies the error type, identifies related files, and proposes up to three root-cause hypotheses with concrete fix plans.

非自明なタスク（3ステップ以上、アーキテクチャ判断、複数ファイルにまたがる変更）に取り組む際の計画・実行・検証サイクル。タスクの開始時、実装がうまくいかず再計画が必要な時、バグ修正やリファクタリングの着手時にこのスキルを参照する。「計画を立てて」「TODO を整理して」「この機能を実装して」「バグを直して」といったリクエストや、明らかに複数ステップを要するタスクではこのスキルを使う。ただし、大規模な新機能開発（コードベース探索・アーキテクチャ設計・並列レビューが必要な重量級タスク）には feature-dev プラグイン（/feature-dev）の方が適切。

This skill should be used when the user asks to "最小再現環境を作って", "再現環境を構築して", "問題を切り分けたい", "パッケージの不具合か確認したい", "create a minimal reproduction", "isolate the issue", "build a repro environment", "reproduce this bug", "narrow down the cause", "is this a package bug or my code", "このPRの問題を再現して", "this commit broke something", or wants to determine whether a bug is caused by a package, the environment, or application code. Accepts PR URLs, commit hashes, or branch names as input.

Route a PR review request to the correct tool — code-review plugin (quick parallel scan across all dimensions) or pr-review-toolkit (deep-dive on a specific quality dimension such as type design, error handling, test quality, comments, or simplification). Use when the user asks for a code review, PR review, or mentions a specific quality concern before creating a PR.

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。

This skill should be used when the user asks to "sandboxの互換性をチェックして", "sandbox設定を確認して", "このプロジェクトでsandboxが使えるか調べて", "sandboxでコマンドが失敗する", "check sandbox compatibility", "verify sandbox settings", "sandbox is blocking my commands", or wants to ensure their development workflow works within Claude Code's sandbox restrictions — either proactively before starting work or reactively after encountering sandbox-related failures.

Guide the user through starting a new web application project — elicit requirements (MoSCoW scoping), create architecture and requirements documents, break work into tasks, and register them as a GitHub Project kanban board. Use when the user says "新しいWebアプリを作りたい", "Webアプリの立ち上げを手伝って", "start a new web app project", "プロジェクトの要件を整理したい", or "GitHub Projectにタスクを登録したい".

This skill should be used when the user asks to "プロジェクトを解析して", "コードベースを調べてドキュメント化して", "移行作業の準備をして", "新機能実装の前にプロジェクトを整理して", "analyze this codebase", "document the project structure", "既存プロジェクトのCLAUDE.mdを作って", or wants to prepare CLAUDE.md and architecture docs before a migration, feature development, or onboarding.

Explain selected code or a specified file/function in plain language, including what it does, why it exists, and potential pitfalls

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。