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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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。

Universal LaTeX document skill: create, compile, and convert any document to professional PDF with PNG previews. Supports resumes, reports, cover letters, invoices, academic papers, theses/dissertations, academic CVs, presentations (Beamer), scientific posters, formal letters, exams/quizzes, books, cheat sheets, reference cards, exam formula sheets, fillable PDF forms (hyperref form fields), conditional content (etoolbox toggles), mail merge from CSV/JSON (Jinja2 templates), version diffing (latexdiff), charts (pgfplots + matplotlib), tables (booktabs + CSV import), images (TikZ), Mermaid diagrams, AI-generated images, watermarks, landscape pages, bibliography/citations (BibTeX/biblatex), multi-language/CJK (auto XeLaTeX), algorithms/pseudocode, colored boxes (tcolorbox), SI units (siunitx), Pandoc format conversion (Markdown/DOCX/HTML ↔ LaTeX), and PDF-to-LaTeX conversion of handwritten or printed documents (math, business, legal, general). Compile script supports pdflatex, xelatex, lualatex with auto-detection, latexmk backend, texfot log filtering, PDF/A output, and verbosity control (--verbose/--quiet). Empirically optimized scaling: single agent 1-10 pages, split 11-20, batch-7 pipeline 21+. Use when user asks to: (1) create a resume/CV/cover letter, (2) write a LaTeX document, (3) create PDF with tables/charts/images, (4) compile a .tex file, (5) make a report/invoice/presentation, (6) anything involving LaTeX or pdflatex, (7) convert/OCR a PDF to LaTeX, (8) convert handwritten notes, (9) create charts/graphs/diagrams, (10) create slides, (11) write a thesis or dissertation, (12) create an academic CV, (13) create a poster, (14) create an exam/quiz, (15) create a book, (16) convert between document formats (Markdown, DOCX, HTML to/from LaTeX), (17) generate Mermaid diagrams for LaTeX, (18) create a formal business letter, (19) create a cheat sheet or reference card, (20) create an exam formula sheet or crib sheet, (21) condense lecture notes/PDFs into a cheat sheet, (22) create a fillable PDF form with text fields/checkboxes/dropdowns, (23) create a document with conditional content/toggles (show/hide sections), (24) generate batch/mail-merge documents from CSV/JSON data, (25) create a version diff PDF (latexdiff) highlighting changes between documents, (26) create a homework or assignment submission with problems and solutions, (27) create a lab report with data tables, graphs, and error analysis, (28) encrypt or password-protect a PDF, (29) merge multiple PDFs into one, (30) optimize/compress a PDF for web or email, (31) lint or check a LaTeX document for common issues, (32) count words in a LaTeX document, (33) analyze document statistics (figures, tables, citations), (34) fetch BibTeX from a DOI, (35) convert a Graphviz .dot file to PDF/PNG, (36) convert a PlantUML .puml file to PDF/PNG, (37) create a one-pager/fact sheet/executive summary, (38) create a datasheet or product specification sheet, (39) extract pages from a PDF (page ranges, odd/even), (40) check LaTeX package availability before compiling, (41) analyze citations and cross-reference with .bib files, (42) debug LaTeX compilation errors, (43) make a document accessible (PDF/A, tagged PDF), (44) create lecture notes or course handouts, (45) fill an existing PDF form (fillable fields or non-fillable with annotations), (46) extract text or tables from a PDF (pdfplumber, pypdf), (47) OCR a scanned PDF to text (pytesseract), (48) create a PDF programmatically with reportlab (Canvas, Platypus), (49) rotate or crop PDF pages (pypdf), (50) add a watermark to an existing PDF, (51) extract metadata from a PDF (title, author, subject).

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Score how hard a keyword is to rank for in the AI-search era — page-level URL Rating of real competitors (not just domain DR), Ahrefs keyword difficulty, and whether a given site already ranks or is cited in Google's AI Overview. Use when the user asks 'how hard is <keyword> to rank', 'geo difficulty for <keyword>', or 'keyword difficulty for <domain>'.

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Creates a lesson plan, student-facing materials, and observation template. Load this skill BEFORE asking the teacher any clarifying question about grade, subject, topic, standard, or timing. Use when a K-12 teacher needs a math, ELA, science, or social studies lesson built from scratch — even if grade, subject, or topic isn't yet stated. Do NOT load for grading, a rubric, assessment feedback, a quiz, or a standards lookup — answer those directly. Triggers on explicit requests (lesson plan, mini-lesson, unit plan, daily plan) and implicit teacher intent: "I'm teaching long division to 5th graders," "need to teach photosynthesis tomorrow." Core signal: teacher needs new instructional content created. A new lesson that asks for differentiated, tiered, or leveled materials is still ONE planning request — this skill produces those materials inside the lesson package; do not also invoke k12-lesson-differentiation. Not for differentiating an existing lesson (use k12-lesson-differentiation) or passage rewrites.

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Pick an LM output format per (task x consumer x model) rather than by reflex: different formats carry different cognitive load (e.g. code-in-JSON makes the same model write worse code than plain-text+diff, while asking for prose when you need a typed object fails the other way). Use when designing or debugging an LM's output schema, choosing between plain text / diff / JSON / tool-call / grammar-constrained output, or when a model's quality drops after wrapping its output in a structured format.

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Use Diffusion Planner for nuPlan autonomous-driving trajectory generation: prepare model-ready data, train or resume the diffusion model, configure closed-loop planning, and add differentiable collision or classifier guidance.

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Use audio-diffusion-pytorch for PyTorch waveform diffusion generators, text-conditioned audio generation, inpainting, upsampling, vocoding, and diffusion autoencoding.

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。

Diff a live page's accessibility violations against a baseline — by default compares uncommitted changes (stash-based), or pass --branch [<name>] to diff against a branch. Reports only new violations introduced, violations fixed, and pre-existing count. Use `scan` for a full audit with no diffing.

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Deploy differential privacy in production systems including epsilon selection strategies, noise calibration with Laplace and Gaussian mechanisms, privacy budget tracking, composition theorems, and Python implementation patterns. Covers both central and local differential privacy models.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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 protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold or chai. For QC thresholds, use protein-qc.

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All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For backbone-only generation, use rfdiffusion. For sequence-only design, use proteinmpnn. For structure validation, use boltz.

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Maps the `hunkdiff/extension` authoring surface for Hunk, the terminal diff viewer — hiding or reordering reviewed files, docked panes, alternate file views, commands and key bindings, dialogs, workspace writes, themes, syntax languages, VCS backends, lifecycle events. Use when writing, debugging, or installing a Hunk extension, or when a request asks Hunk itself to behave differently. Not for reviewing a diff in a live session — that is hunk-review.

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Fit cognitive drift-diffusion models (Ratcliff DDM) to reaction time and accuracy data with parameter estimation (drift rate, boundary separation, non-decision time), model comparison, and parameter recovery validation. Use when modeling binary decision-making with reaction time data, estimating cognitive parameters from experimental data, comparing sequential sampling model variants, or decomposing speed-accuracy tradeoff effects into latent cognitive components.

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See the difference between Chat and Cowork with a live side-by-side comparison for understanding why Cowork is built differently. Use when evaluating AI tools, for comparing chat versus agent capabilities, during an AI tool decision, when switching from ChatGPT or Claude Chat, or when the user says "what is different about cowork", "cowork vs chat", "why not just use chatgpt", "show me the difference", "compare chat and cowork", or "why should I use cowork instead of chat".

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Run a Duck Critic producer-critic loop: you (main) keep producing the plan/code/tests and gate your own work at checkpoints with a different-model critic, revising until it passes. Use when asked for rubber duck, ラバーダック, 別モデルレビュー, second opinion, critic, or a different-model code review, design review, plan critique, or review by another model/agent harness. Not for readability refactoring or code cleanup alone.

Compares two related malware samples to surface what changed between variants using section-level hashing, import-set differences, and fuzzy similarity scoring. Activates for requests to diff two samples, compare malware variants, or measure similarity between two binaries for variant tracking.

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Causal inference with treatment/control groups over time. Use when user mentions: treatment effects, policy evaluation, pre/post comparison, parallel trends, DID, DiD, difference in differences, natural experiment, quasi-experimental.

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。

Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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。

Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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。

Diff a live page's accessibility violations against a baseline — by default compares uncommitted changes (stash-based), or pass --branch [<name>] to diff against a branch. Reports only new violations introduced, violations fixed, and pre-existing count. Use `scan` for a full audit with no diffing.

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。

Expert-level differential equations knowledge. Use when working with ordinary differential equations, partial differential equations, systems of ODEs, Laplace transforms, Fourier methods, boundary value problems, stability analysis, or numerical methods for ODEs. Also use when the user mentions 'ODE', 'PDE', 'initial value problem', 'boundary value problem', 'Laplace transform', 'separation of variables', 'eigenvalue problem', 'heat equation', 'wave equation', 'Laplace equation', 'stability', or 'phase plane'.

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spec-drift issue が起票され diff トリアージが必要なとき、C11 が再構成した issue 単位の完全 diff を hunk 化し name/type/required/enum/semantics 各軸の影響を before/after/evidence 付きで判定して triage-report を出したいときに使う。