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Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.

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Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have poor quality tails or require minimum quality for downstream analysis.

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Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.

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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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Review skills in any project using a dual-axis method: (1) deterministic code-based checks (structure, scripts, tests, execution safety) and (2) LLM deep review findings. Use when you need reproducible quality scoring for `skills/*/SKILL.md`, want to gate merges with a score threshold (for example 90+), or need concrete improvement items for low-scoring skills. Works across projects via --project-root.

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Use when the user asks to "build our social crisis protocol", "mentions are exploding — what do we do first", or "when do we pause the posting queue"; produces a 1-5 severity ladder with tunable Estimated trigger thresholds (mention-velocity multiples vs the 7-day listening baseline, sentiment flip, journalist/regulator contact, employee-conduct class), the first-mechanical-action rule — pause ALL scheduled posts AND paid amplification, with dated state markers dropped to the channels proposal protocol and reconciled post-incident — a pre-approved holding-statement library with committed update cadences, when-NOT-to-post rules, a spokesperson/approval matrix, and a post-crisis retro template; re-runs the social-quality-auditor pre-publish gate before un-pausing the queue. Not for email deliverability incidents (blocklist, spam-rate spikes) — use deliverability-qa; inside a launch window launch-day-conductor owns incident handling. 社媒危机预案/暂停队列/声明库/发言人矩阵

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Use when the user asks to "monitor my launch", "track our Product Hunt / Hacker News ranking", or "watch the launch window"; runs the T-0 to T+30 window watch — pre-launch instrumentation verification (UTM/event checks, the upstream of RAMP P1), HN rank/points/comments polling with a comments-over-points flamewar early-warning (Estimated heuristic), PH votes/featured status, store charts and reviews, news echo, D0/W1/M1 KPI snapshots vs targets, spike-vs-sustain and owned-capture reads, and alert thresholds against the launch-tier KPI targets. Not for launch-day go/rollback calls — use launch-day-conductor; not for metric deep-dives — use performance-analyzer; not for SEO rank tracking — use rank-tracker. 发布监控/排名轮询/火焰战比/spike-sustain

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Use when the user asks to "plan my launch tier", "how big should this launch be", or "build a launch risk register with kill criteria"; produces a tier decision (Tier 1 flagship all-channel / Tier 2 targeted / Tier 3 changelog-level), a launch-type declaration (new-product / feature / relaunch / partnership with co-marketing split), an effort calibration matrix (tier to channel intensity and asset scope), D0/W1/M1 KPI targets (labeled Estimated), a risk register (likelihood x blast-radius, owners, mitigations, kill criteria / rollback thresholds), and a T-8w to T+4w timeline skeleton. Not for picking the launch date or window — use launch-window-planner; not for creator-channel launch campaigns — use campaign-planner. 发布分级/发布类型/风险登记册/kill criteria

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Use when the user asks to "generate an SEO report", "出月报", "set SEO alerts", or "排名掉了提醒我"; two modes — report builds multi-metric traffic/ranking/authority/content dashboards, and alert configures threshold notifications for future ranking, traffic, technical, backlink, competitor, and AI-visibility changes. Not for raw position-by-position deltas — use rank-tracker. SEO报告/绩效仪表盘/SEO预警/排名监控

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Use when the user asks to "test our messaging before we scale it", "design a message-market-fit panel", or "run a 5-second comprehension test on our new tagline"; produces a message-test design spec — hypothesis, panel and recruit criteria, comprehension / 5-second / message-market-fit (Wynter-style) protocols, stimulus set drawn from the canon, success thresholds, and a stop/revise decision rule — for the TALE Evaluate phase so the message is validated before any paid scale. It designs the test; it never runs the experiment or adjudicates a claim. Not for running the panel or A/B experiment — use send-experiment-designer or ad-test-designer; not for analyzing the results — use performance-analyzer; not for authoring the message itself — use message-system-architect. 消息测试/理解度测试/面板设计/五秒测试/消息市场契合

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Design waiting experiences — spinners, skeletons, optimistic updates, and progressive reveal. Use when content takes time to arrive. For the latency budget itself use `doherty-threshold`; for success confirmation use `feedback-patterns`.

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Audit a Node.js project's installed npm dependency tree for known CVEs by wrapping the npm audit JSON output and emitting findings in the canonical penetration-tester schema. Detects direct AND transitive vulnerabilities, normalizes npm's severity scale (info/low/moderate/ high/critical) to the shared Severity enum, and parses both v1 and v2 audit output formats so the skill works against npm 6 and npm 7+ lockfiles. Use when: pre-merge gate on a Node project, post-incident sweep after a transitive package compromise (e.g. event-stream, ua-parser, node-ipc, color.js), SOC2 vendor-management evidence collection, or auditing an inherited or acquired Node codebase. Threshold: any HIGH or CRITICAL CVE in the resolved dependency tree. MODERATE / LOW reported informationally. Trigger with: "audit npm deps", "npm vulnerability scan", "check node packages for CVEs", "npm audit".

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Audit a target's CORS posture — Access-Control-Allow-Origin handling, reflected-origin bypass, credentials+wildcard mismatch, preflight OPTIONS behavior, Vary header correctness. Use when: a third-party integration is failing CORS preflight and someone proposes "just set Allow-Origin to *" as the fix, OR your bug-bounty inbox has a credential-reuse exploit chain. Threshold: any reflection of arbitrary Origin into Allow-Origin, Allow-Credentials:true with wildcard origin (browser-rejected combo but server config wrong), missing Vary:Origin on per-origin responses, preflight cached over 86400s, OR Allow-Origin trust of attacker- controlled subdomain pattern. Trigger with: "audit cors", "check cors policy", "cors bypass", "preflight check".

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Audit a Python project's installed dependencies for known CVEs by wrapping pip-audit (PyPA's official vulnerability auditor) and emitting findings in the canonical penetration-tester schema. Detects vulnerable direct AND transitive packages, normalizes pip-audit's severity output via OSV severity bands, falls back to pip list --outdated when pip-audit isn't installed, and supports requirements.txt, pyproject.toml (PEP 621), Pipfile.lock, and poetry.lock as input sources. Use when: pre-merge gate on a Python project, post-incident sweep after a PyPI compromise (e.g. ctx, request-toolbelt typosquats, ultralytics 8.3.42 compromise), SOC2 evidence collection, or inheriting an unfamiliar Python codebase. Threshold: any HIGH or CRITICAL CVE in the resolved dependency tree. MODERATE / LOW reported informationally. Trigger with: "audit python deps", "pip vulnerability scan", "check pypi packages for CVEs", "pip-audit run".

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Analyze a target's TLS configuration — negotiated protocol version, cipher suite, certificate chain, expiry, and downgrade vectors. Use when: SOC2 auditor flagged your endpoint for "weak TLS" but you don't know which control failed (TSC CC6.7 transmission integrity vs CC6.6 encryption) or which cipher is the problem. Threshold: any negotiated TLSv1.0 or TLSv1.1, OR a cipher with RC4 / 3DES / null / EXPORT, OR a cert with under 30 days to expiry, OR a chain that fails hostname verification. Trigger with: "audit tls", "check ssl config", "weak tls", "analyze tls".

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Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

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Turn a raster logo (PNG/JPG/WebP/screenshot) into a clean minimal SVG with edge smoothness as the primary hard gate and IoU optimized as high as reasonably possible without a fixed global threshold, then into a choreographed logo animation delivered as standalone JS-rendered HTML, applying Disney's 12 animation principles. Use when asked to animate a logo, build a logo reveal / splash screen / brand intro, convert a logo image into animated SVG or HTML, add motion to a vectorized mark, or create loading/idle/hover motion for a brand mark. v2: also handles self-crossing draw-on choreography (split-fill, exact easing subdivision, tip glint), closed variable-width ribbon fitting, and quantitative motion QA (easing probe, ink-delta continuity sweep).

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Extract, suggest, and sync tags and categories for blog posts across all major CMS platforms. Supports WordPress REST API, Shopify GraphQL, Ghost Content API, Strapi REST/GraphQL, and Sanity GROQ. Generates tag suggestions from content analysis (keyword frequency, heading extraction, semantic grouping), enforces minimum post-count thresholds to prevent thin tag archives, and syncs taxonomy via authenticated API calls. Use when user says "tags", "categories", "taxonomy", "tag suggestions", "sync tags", "WordPress tags", "Shopify tags".

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When the user wants to set up, debug, or interpret app install attribution — including SKAdNetwork (SKAN), Apple's AdAttributionKit, Google Play Install Referrer, MMPs (AppsFlyer, Adjust, Singular, Branch, Kochava), deep links, deferred deep links, conversion values, postback windows, or privacy thresholds. Use when the user mentions "SKAdNetwork", "SKAN", "SKAN 4", "AdAttributionKit", "AAK", "MMP", "AppsFlyer", "Adjust", "Singular", "Branch", "attribution", "conversion value", "postback", "Install Referrer", "deferred deep link", "iOS 14.5", "ATT", "App Tracking Transparency", "IDFA", or "I can't measure my ad campaigns". For paid campaign strategy, see ua-campaign and apple-search-ads. For analytics events, see app-analytics.

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Defines and manages service levels — setting targets that reflect what customers need, measuring honestly, and handling breaches. Use this to write or negotiate an SLA, decide what to measure and at what threshold, respond to a missed service level, or work out why a service that meets its targets still has unhappy customers.

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Reviews and negotiates commercial agreements — MSAs, SOWs, order forms, NDAs, vendor and data-processing agreements — identifying material risk, proposing positions, and recommending a path rather than listing issues. Use this to review a contract before signature, prepare a negotiation position, build fallback positions and approval thresholds, or assess exposure in terms already agreed.

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Designs and tests controls over financial reporting — segregation of duties, approval limits, evidence, and preparing for audit. Use this to design controls for a process, prepare for an external audit, respond to an audit finding, set approval thresholds, or assess where a small team's segregation of duties is genuinely broken.

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