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Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.

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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).

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提供在WinForms中通过ElementHost嵌入DiffPlex的WPF DiffViewer控件，实现两个字符串的对比及差异高亮显示的代码方案。

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Generate and interpret security-research diffs between Windows versions or patch levels using this repo's WinDiff CLI and databases. Use when comparing Windows builds or binaries such as ntoskrnl.exe, ntdll.dll, win32k*.sys, ci.dll, or cng.sys to find changed syscalls, symbols, types, mitigation flags, callbacks, ETW/EtwTi telemetry, code-integrity behavior, drivers, or attack surface. Explain likely intent and security relevance with Windows-internals knowledge, and frame findings for anti-malware/EDR, anti-cheat, and vulnerability-research audiences rather than returning an uninterpreted symbol list.

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Use denoising-diffusion-pytorch for PyTorch DDPM/DDIM image diffusion, 1D sequence diffusion, conditioning and guidance, and advanced diffusion variants.

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N-day / patch-diff workflow - given a CVE/advisory or a suspicious patch, diff pre- vs post-patch to locate the fixed bug, build a PoC for the unpatched version, and run variant analysis for a fresh bug. Triggers - "n-day", "patch diff", "diff the patch", "bindiff".

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Use Pierre Computer Company's `@pierre/trees` (path-first file tree) and `@pierre/diffs` (shiki-based code/diff renderer) in Kolu. Pierre ships Preact/vanilla cores with optional React wrappers — Kolu consumes the vanilla classes and wraps them in thin SolidJS components. Trigger when: wiring up a file tree, rendering unified diffs or syntax-highlighted files, replacing `@git-diff-view`, or any mention of `@pierre/trees` / `@pierre/diffs` / "pierre library".

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Implement a generative diffusion model (DDPM or score-based) with noise scheduling, U-Net architecture, training loop, and sampling procedures including DDIM acceleration. Use when building a generative model for image, audio, or molecular synthesis; implementing DDPM from a research paper; adding a custom noise schedule or conditioning mechanism; replacing a GAN-based generator with a diffusion alternative; or prototyping before scaling with production frameworks like diffusers.

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Analyze pre-trained generative diffusion models (Stable Diffusion, DALL-E, Flux) by computing quality metrics (FID, IS, CLIP score, precision/recall), inspecting noise schedules, extracting and visualizing attention maps, and probing latent spaces. Use when evaluating a pre-trained generative diffusion model's output quality, comparing noise schedule variants, analyzing cross-attention patterns for text-conditioned generation, interpolating between latent codes, or detecting out-of-distribution inputs.

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Before committing any non-trivial change, dispatch the diff to a reviewer runtime via ATO (`ato dispatch <reviewer> --session <id>`), parse the numbered/severity-tagged findings, apply or defer each one with a recorded justification, then commit. Fights the "build passes therefore ship it" failure mode — what Garry Tan calls the AI agent complexity ratchet. Place in the v2.16 stack: this skill is the LAST gate. `ato-warroom` decides the design; `ato-mission` runs the multi-step work and produces the diff; `ato-review` checks the diff before commit. When the review is part of a Mission, dispatch the review with `--require-tools read_file,grep,git_diff,git_log` so the reviewer can walk the source itself instead of reasoning from a paraphrase (PR-1.5 tool surface). Receipts land in `execution_logs` and the Mission narrative. Fires automatically before commits touching public surface (CLI subcommands, Tauri commands, MCP tools, schema migrations, security boundaries) or whenever a diff exceeds ~50 LOC of behavior change.

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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).

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Geração de imagens com tecnologia de ponta usando Stable Diffusion via HuggingFace Diffusers. Use quando gerar imagens a partir de prompts em texto, realizar tradução de imagem para imagem, inpainting ou construir pipelines de difusão customizados.

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Install or synchronize BMS差分 from a beatoraja-compatible difficulty table, optionally download missing parent songs, and place charts into matching music folders without overwriting existing files. Use for 難易度表 URL, header.json, url_diff, or beatoraja差分 installation requests; do not use for ordinary BMS library organization unrelated to a difficulty table.

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PR・ブランチの変更差分（git diff）を静的解析してセキュリティ脆弱性を検出する。開発中・PRレビュー時に使用。手動呼び出し専用: /sec-diff-review

提供在WinForms中通过ElementHost嵌入DiffPlex的WPF DiffViewer控件，实现两个字符串的对比及差异高亮显示的代码方案。

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Review code changes from the current branch, staged changes, a git ref, or a diff/patch file. Pure git-native — no platform/PR awareness. Trigger when user says "review this", "review diff", "/aiwork:code-review-diff", or provides a git ref or diff path. Read-only — never posts comments.

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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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Converts a markdown PR writeup or code review (one with ```diff fenced blocks and severity-tagged > [!BLOCKER]/[!MAJOR]/[!MINOR]/[!NIT] callouts) into a single-file 2-column HTML review — unified-diff on the left, severity-tagged annotation cards on the right, top jump-nav listing every finding, mandatory named reviewer footer. Triggers when the markdown-html-orchestrator classifies an input as REVIEW, or when invoked directly via /cs:md-review. Refuses without explicit --reviewer (a code review must name a human), refuses if no diff hunks present (route to md-document instead), and refuses to encode severity in color only (every badge ships color + icon + aria-label per WCAG 1.4.1). Use after orchestrator routing.

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Hunt shadow / zombie / undocumented API surface (OWASP API9 Improper Inventory Management) — enumerate the full API version history (v1/v2/beta/legacy paths, header- and subdomain-based versioning), pull and diff every reachable OpenAPI/Swagger spec (including ones only findable via the Wayback Machine), and behaviorally diff old vs. current versions for auth/rate-limit/validation regressions rather than just response-shape differences. Distinct from hunt-api-misconfig, which owns exploitation once you have a spec or endpoint (mass assignment, JWT, OData, Swagger-chain attacks); distinct from hunt-subdomain, which owns host-level discovery. This skill owns the version-inventory and behavioral-diff workflow itself. Use when the target has versioned API paths, multiple specs, a changelog referencing deprecated endpoints, or a mobile app whose hardcoded backend calls look older than the current web app's.

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This skill covers causal inference methods in observational and quasi-experimental settings. Use when the user is implementing, choosing between, or debugging causal identification strategies — including instrumental variables, difference-in-differences, regression discontinuity, synthetic control, or matching estimators. Triggers on "causal effect", "identification strategy", "instrumental variable", "2SLS", "GMM", "difference-in-differences", "DiD", "staggered treatment", "regression discontinuity", "RDD", "synthetic control", "matching", "propensity score", "IPW", "AIPW", "doubly robust", "LATE", "ATT", "ATE", "parallel trends", "exclusion restriction", "first stage", "weak instruments", or "endogeneity".

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Use this skill whenever the user wants to conduct an event study, create event study plots, test for parallel trends, implement difference-in-differences designs, or work with any panel data estimation that involves pre/post treatment comparisons. Trigger on phrases like "event study", "parallel trends", "pre-trends", "dynamic treatment effects", "leads and lags", "TWFE", "two-way fixed effects", "staggered adoption", "staggered treatment", "difference-in-differences", "DiD", "Sun and Abraham", "Callaway and Sant'Anna", "de Chaisemartin", "Borusyak", "did_multiplegt", "fixest", "did2s", "bacon decomposition", or any reference to plotting coefficients around a treatment event. Also trigger when the user uploads panel data and wants to estimate treatment effects with variation in treatment timing. All code is in R.

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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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Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.

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Turns one-shot external recon into a continuous monitoring program. Covers the scheduled re-scan-and-diff loop (baseline snapshot -> interval sleep -> re-scan -> asset/finding delta -> threshold-gated webhook alert), the scan-to-scan diff engine (new/removed/changed assets by a tracked-attribute table, new/resolved findings by a stable cross-scan fingerprint), adversary CTI / chatter monitoring across six public feeds (ransomwatch, ransomware.live, HackerNews Algolia search, Reddit security-subreddit RSS, GitHub Gist code-search, public Telegram channel scraping) with a source-kind-aware severity engine (leak-site/forum/telegram/paste tiers, CRITICAL through INFO), literal/glob/regex watchlist pattern matching, full-corpus capture with retroactive rescan on new watchlist entries, infrastructure-tracking-over-time discipline (certificate-transparency, passive-DNS, port/service, and typosquat re-enumeration cadence, and what a genuine 'perimeter drift' event looks like in the diff output), a five-state finding-lifecycle state machine (open/triaged/risk_accepted/resolved/false_positive) with per-severity SLA and fingerprint-based cross-scan dedup and auto-resolve/reopen rules, the alert-fatigue trap where a lifecycle-unaware rule re-fires on an already-accepted finding, a durable retry/backoff alert-outbox pattern ('queued is not delivered'), and copy-paste bash-cron plus PowerShell-Scheduled-Task recipes for a re-scan+diff loop with the Slack-compatible webhook payload shape. Passive OSINT and analysis only -- no new active-intrusion technique. Use when setting up ongoing monitoring for a retainer or MSSP engagement, tuning alert thresholds to avoid fatigue, triaging a finding's lifecycle status, investigating adversary chatter about a brand, building a 'what changed on the perimeter since last week' report, or deciding whether a persisting finding should re-alert.

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