「diff」の検索結果

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.

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Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.

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Workflow track for tasks that need no TDD — documentation edits, governance count bumps, vendored-skill content updates, configuration tweaks, formatting, typo fixes, dependency bumps where no project code changes. Skips `/scenario` and `/implement` (no failing test to drive) and runs the work directly. `archive`, `memory-sync`, `/grant-commit`, and `/commit` remain mandatory. `verify`, `simplify`, `integrate`, and `document` are conditional — required when the diff hits one of the listed triggers, optional otherwise. `verify` is skipped only when the diff is pure-docs/prose AND `project.json → test.kind` is `behavior` (absent/invalid `test.kind` → `structural` → verify runs). Chore is a stripped-down pipeline, not a bypass; never silently skip a conditional phase whose triggers apply.

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Diagnose why an existing implementation differs from reference evidence using AE/SSIM, pixel, section, computed-style, and transition diffs. Use for post-implementation mismatch or repair guidance; not baseline capture or full clone generation.

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Analyze the current uncommitted diff and give a detailed summary with risk assessment. Use when asking what changed, reviewing changes before a commit, or requesting a change summary.

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Expert-level mass transfer covering molecular diffusion, convective mass transfer, interphase transfer, mass transfer coefficients, and design of mass transfer equipment.

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Expert-level optics knowledge. Use when working with geometric optics, wave optics, interference, diffraction, polarization, lasers, fiber optics, optical instruments, or photonics. Also use when the user mentions 'reflection', 'refraction', 'Snell law', 'lens', 'mirror', 'interference', 'diffraction', 'polarization', 'laser', 'fiber optic', 'holography', 'aberration', or 'optical instrument'.

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Expert-level numerical methods knowledge. Use when working with root finding, numerical integration, numerical differentiation, interpolation, numerical linear algebra, ODEs, PDEs, or optimization algorithms. Also use when the user mentions 'Newton method', 'bisection', 'Runge-Kutta', 'finite difference', 'finite element', 'interpolation', 'numerical integration', 'quadrature', 'iterative solvers', 'condition number', 'round-off error', or 'truncation error'.

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Read-only reviewer for agent-flow. Judges one diff against the acceptance criteria, AGENTS.md rules, protected paths and risk boundaries; returns a JSON verdict with line-anchored findings. Use when launched with AGENT_FLOW_ROLE=reviewer or asked for an agent-flow review of a diff.

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Use when reviewing PRs/diffs/branches/documents for .NET quality, correctness, performance, security, data access, messaging, and observability. Includes adversarial critical-thinking mode for skeptical/cynical review requests. Keywords: code review, review PR, review diff, critical review, cynical review, adversarial review, production readiness, low GC, AOT, security review.

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日本語の文章 (Markdown・テキスト) から「AI 臭さ」(LLM の文章に特有の定型句・単調な文のリズム・ 見出しと箇条書きだけの体裁) を検出する CLI。日本語の文章を書いた・直した後の見直し、 AI が書いたような文を自然にしたいとき、推敲・校正・AI っぽさのチェック、改稿の前後の比較 (数字や固有名詞が消えていないか・同じ直しを一律に当てていないか) の場面で発動。コードに書いた 日本語のコメント・静的な文字列・JSX/HTML の表示文言 (コードのファイルも直接検査できる) や、gws で Google ドキュメント・スプレッドシートに書き込む文章の見直し、noslop のフックが指摘を返した・ gws の書き込みを止めたときの対応にも使う。 noslop check --report brief --format toon で直す箇所を少ないトークンで受け取り、 改稿のルールに従って効果の大きい箇所だけを直す。直した後は noslop diff で 1 回だけ確かめる。

Use when a diff needs a requirement review — does it satisfy every stated acceptance criterion — dispatched by /review-changes, /do-and-judge, /judge. Never infers criteria from the diff.

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[Code Quality] Use when you need to combine /changes-review + /fix in a recursive loop — each round runs /changes-review (report-only) to surface validated findings over a fixed diff scope, then /fix to resolve them, then loops again with a FRESH full /changes-review over the CHANGED diff until one complete pass produces zero validated findings (nothing left to fix).

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Generate AI music and songs with Diffrythm, Tencent Song Generation via inference.sh CLI. Models: Diffrythm (fast song generation), Tencent Song Generation (full songs with vocals). Capabilities: text-to-music, song generation, instrumental, lyrics to song, soundtrack creation. Use for: ba...

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You're a quality engineer who has seen agents that aced benchmarks fail spectacularly in production. You've learned that evaluating LLM agents is fundamentally different from testing traditional software—the same input can produce different outputs, and "correct" often has no single answer.

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Run the Tamanu release-branch CUTOFF checks when preparing to cut a new release/X.YY branch: confirm the previous release's hotfixes are merged to main, reconcile the commits since the previous release against the "Merged to main" card list from Linear, and scan for data/reporting/schema changes. Use when the user is cutting a Tamanu release and wants to verify the codebase is ready, wants to check main against the previous release branch, or wants to reconcile commits with a Linear "Merged to main" column (they should paste the card list). Handles Tamanu's train-release model (release/X.YY branches vs vX.YY.Z patch tags) and the cherry-pick model where the same logical fix has different SHAs on different branches. Purely git-based — no live database or Canopy access needed. Not for verifying an existing release branch's hotfix integrity (see pre-release-checks) or for deciding which tests to run (see scope-tamanu-release-tests).

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Run Tamanu pre-release verification checks: verify that hotfixes on the current release branch are merged forward to main, and that hotfixes from prior release branches are included in the current release. Use when the user wants to run "pre-release checks", verify hotfix integrity before cutting or shipping a Tamanu release, confirm a release/X.YY branch is safe to release, or check that no hotfix has been orphaned (left on neither main nor the current release). Handles Tamanu's train-release model (release/X.YY branches vs vX.YY.Z patch tags) and the cherry-pick model where the same logical fix has different SHAs on different branches. Purely git-based — no live database or Canopy access needed. Not for deciding which tests to run (see scope-tamanu-release-tests).

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Check upgrade safety for a Tamanu upgrade that spans many versions: verify that every intermediate hotfix is included in the target version, and surface the new configuration/settings, data migrations, and FHIR rematerialisation impact the upgrade brings. Use when the user wants to check an upgrade from one Tamanu version to another (e.g. "check hotfixes from v2.31 to v2.47"), confirm no intermediate hotfix was dropped, or understand what config, migrations, and FHIR rework a multi-version jump requires. Handles Tamanu's train-release model (release/X.YY branches vs vX.YY.Z patch tags) and the cherry-pick model where the same logical fix has different SHAs on different branches. Purely git-based — no live database or Canopy access needed. Not for cutting a release (see release-cutoff-checks) or deciding which tests to run (see scope-tamanu-release-tests).

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ローカルの変更差分（git diff）を3つのサブエージェントで並列レビューし、結果を統合して修正を適用する。PR作成前やタスク完了前のローカル品質チェックに使用する。ai-code-reviewと同一の6観点・重大度基準を適用する。

Heuristic-first software surgery for proof-backed, minimal-diff implementation: Contract to Invariants to Cut Rationale to inevitable incision to Proof. Use when users say "run /tw-tk", "patch-first", "keep the diff small", "state contract + invariants", "one clear incision", "fix it with a validation signal", or orchestration cues like "workers use /tw-tk" / "internally use /tw-tk".

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。