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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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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.

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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.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Use when building ANY macOS app — windows, menus, sandboxing, distribution, AppKit bridging or modernization (control events, state restoration, concentric corners), or macOS-specific SwiftUI patterns.

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在 Windows/macOS/Linux 上使用 `uv` 执行 Python 运行、依赖同步、锁文件管理、Python 版本管理与工具命令（`uv run`、`uv sync`、`uv lock`、`uv python`、`uv tool`）。当任务涉及“用 uv 运行脚本/命令”“临时依赖（`--with`）”“锁文件一致性（`--locked`/`--frozen`）”“跨平台 shell（bash/zsh/PowerShell）下排查 uv 执行问题”时使用此 skill。

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在 Windows PowerShell 5.1 与 PowerShell 7 中编写和执行稳定命令，重点处理引号、管道符、原生命令参数传递与跨版本兼容。遇到 `--jq`/过滤表达式被 PowerShell 误解析、同一命令在 pwsh5 与 pwsh7 行为不一致、或需要为 pwsh7.3+ 增加参数传递适配时使用此 skill。

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Analyze signal spectra in MATLAB using nonparametric and parametric estimators. Use when computing frequency content, PSD, power spectrum, spectral peaks, bandwidth, or streaming spectral analysis. Covers pspectrum, pwelch, periodogram, pmtm, pburg, pmusic, rootmusic, plomb, poctave, spectrumAnalyzer, dsp.SpectrumEstimator. TRIGGER: FFT, PSD, power spectrum, spectral analysis, frequency content, bandwidth measurement, spectral leakage, window selection, streaming spectrum, periodicity, resolve close frequencies, multitaper. DO NOT TRIGGER: filter design, spectrogram/time-frequency, audio features.

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Perform aerospace unit conversions, time conversions, coordinate frame transformations, and rotation representations using Aerospace Toolbox. Use when converting units (length, velocity, angle, acceleration, angular velocity, force, mass, pressure, temperature, density), computing Julian dates or decimal years, transforming between coordinate frames (ECEF, ECI, LLA, flat Earth, geodetic/geocentric, NED, body, wind, stability), or working with rotation representations (Euler angles, DCM, quaternion, Rodrigues vector). Also use when the user asks about aerospace coordinate systems, reference frames, or rotation conventions.

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Manage and secure company devices with MDM solutions — enroll macOS, Windows, iOS, and Android devices, enforce security policies, and automate software deployment. Use when setting up device management for a growing team.

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Implement change management processes. Configure CAB reviews, change windows, and rollback procedures. Use when managing production changes.

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Use when driving a desktop GUI through a computer-use driver — windows, menus, native apps, OS dialogs. You build a table of safe actions; Jev picks the next one in about 0.4 seconds.

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Crabbox/Testbox remote proof: portable provider routing, untrusted isolation, Linux/macOS/Windows/WSL2, live E2E, diagnostics, cleanup.

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Produce a detailed report on APIError events from Agent Monitor data — counts over time, which sessions and models are affected, and the likely root cause (rate limits, overload/529, or context-window pressure) inferred from each event's summary and data payload. Use when API errors spike or when you need to explain why requests are failing.

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Discover when you are most active and most productive with Claude Code by bucketing sessions and events into hour-of-day and day-of-week bins from their timestamps, then flagging peak versus low-output windows. Uses the session list, per-session events, and analytics daily trends. Use when planning a schedule or deciding when to do deep work versus lighter tasks.

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Polls the Agent Monitor /api/stats endpoint several times over a short window and reports the live deltas in active_sessions, active_agents, events_today, and ws_connections so you can see activity moving in real time. Use when watching the dashboard for live changes rather than a one-time snapshot.

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Analyze Claude Code usage trends over time using the Agent Monitor's analytics API — daily session counts, daily event counts, token volumes by type, model distribution, tool usage rankings, and agent/event type distributions across 365-day retention windows.

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Build a full-stack TanStack Start app on Cloudflare Workers from scratch — SSR, file-based routing, server functions, D1+Drizzle, better-auth, Tailwind v4+shadcn/ui. Use whenever the user mentions TanStack Start, asks to scaffold a full-stack Cloudflare app with SSR, wants an SSR dashboard, or asks for a React 19 + Cloudflare Workers app with file-based routing and server functions — even if they don't name TanStack Start specifically. No template repo — Claude generates every file fresh per project.

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Scaffold a full-stack Cloudflare app from the vite-flare-starter template — React 19 + Hono + D1+Drizzle + better-auth + Tailwind v4+shadcn/ui + TanStack Query + R2 + Workers AI. Run setup.sh to clone, configure, and deploy. Use whenever the user wants a batteries-included Cloudflare full-stack app, vite-flare-starter scaffold, or a React + Cloudflare app with auth + database + Workers AI ready to go.

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Generate a complete, deployable landing page from a brief. Produces a single self-contained HTML file with Tailwind CSS (via CDN), responsive design, dark mode, semantic HTML, and OG meta tags. Sections: hero with CTA, features, social proof, pricing (optional), FAQ, footer. Use when building a marketing page, product launch page, coming soon page, or any standalone landing page. Triggers: 'landing page', 'create a page', 'marketing page', 'launch page', 'coming soon page', 'one-page site'.

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Autonomous multi-page site builder using a baton-passing loop. Each iteration reads a task from .design/next-prompt.md, generates a page in HTML/Tailwind, integrates it into the site, verifies visually, then writes the next task to keep the loop alive. Use whenever the user asks to build an entire site autonomously, build all pages of a site, generate multiple pages in sequence, or run a 'design loop' / 'baton loop' / 'autonomous site build' — even if they say 'just keep going' or 'build the next page' or 'next page' mid-flow.

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Install and configure shadcn/ui components for React projects. Guides component selection, installation order, dependency management, customisation with semantic tokens, and common UI recipes (forms, data tables, navigation, modals). Use after tailwind-theme-builder has set up the theme infrastructure, when adding components, building forms, creating data tables, or setting up navigation.

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Generate the dispatcher PCF for a third-party `.ppmplugin` (wrap-runtime) control. Runs `pac pcf init` in the pcf/ subfolder, rewrites ControlManifest.Input.xml from ARCHITECTURE §6, and writes index.ts derived from ARCHITECTURE §4 (message contract), §8 (PCF surface), §9 (error UX) — no placeholders. The bridge dispatches the composite key `<name>/<receiver>` to `NativeModules.<nativeModule>.<method>` via the host-injected `window.PowerApps.NativeExtension.sendAsync` global (never `cordova.exec` — not in the PCF sandbox); also emits a `PowerAppsNativeExtension.d.ts` ambient declaration. Responses are peeled with `extractResponse`. Emits structured JSON debug/error logs. Validated by `npm run build`. **Local only** — does not deploy. Needs only `pac` CLI. Run after the native module exists. Uses npm (not pnpm).

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