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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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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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Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.

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Use when a carrier is evaluating ELD / telematics / dashcam platforms and needs an objective comparison of Samsara, Motive (formerly KeepTruckin), and Geotab. Covers ELD compliance, AI dashcams, driver scoring, integrations, pricing structure, and which fleet profile suits which platform.

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Use this skill when the user asks how to build + manage direct shipper relationships — moving from spot market to dedicated lanes, customer scoring + credit assessment, contract terms, dedicated capacity agreements, KPI reporting, and how to handle customer disputes. Reference standard customer-carrier contract terms.

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Use this skill when the user asks about FMCSA's Crash Preventability Determination Program (CPDP) — how to dispute that a crash was non-preventable, eligible crash types, evidence requirements, how preventability findings affect SMS scoring + safety ratings, the difference between "preventability" and "fault," and the National Crash Preventability Program. Cite FMCSA CPDP guidance.

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Expert in temporal event detection, spatio-temporal clustering (ST-DBSCAN), and photo context understanding. Use for detecting photo events, clustering by time/location, shareability prediction, place recognition, event significance scoring, and life event detection. Activate on 'event detection', 'temporal clustering', 'ST-DBSCAN', 'spatio-temporal', 'shareability prediction', 'place recognition', 'life events', 'photo events', 'temporal diversity'. NOT for individual photo aesthetic quality (use photo-composition-critic), color palette analysis (use color-theory-palette-harmony-expert), face recognition implementation (use photo-content-recognition-curation-expert), or basic EXIF timestamp extraction.

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Audit or design server-side indexes, directories, reputations, or aggregates that are DERIVED from traffic a platform witnesses (chain heads, run verdicts, heartbeats, publish activity) so that consent gates the derivation, not merely the read: no shadow index over non-consenting principals, post-consent-only evidence windows, retention bounds and delete-propagation into derived rows, activity-oracle threat modeling, and audit-logged ranking discretion. Use when building a capability directory / whois from witnessed activity, a reputation ledger from settled outcomes, vitals aggregation across tenants, or any "the yellow pages can't lie because they index signatures" feature. Keywords: shadow index, derived index, consent gates derivation, activity oracle, phone book not a log, delist propagation, ranking weight audit, k-anonymous aggregate, subpoena surface. NOT for the consent-screen UX and scope-ladder mechanics themselves (use local-first-tenancy-boundary), reputation scoring math and Sybil economics (use agent-identity-continuity-reputation), or discovery-layer architecture L1/L2/L3 (use agent-discovery-directories-guilds).

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Aesthetic assessment and design scoring across 6 dimensions. Use for UI critique, design review, visual quality assessment, remix suggestions. Activate on "design critique", "aesthetic review", "UI assessment", "visual quality", "design score", "remix this design". NOT for implementation (use frontend-developer), accessibility-only audits (use color-contrast-auditor), or brand identity creation.

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Validates agent outputs against schemas and quality criteria, scores confidence, detects hallucinations, monitors convergence, decides when to iterate, and synthesizes actionable feedback. Use when checking if a node's output is acceptable, scoring confidence, detecting fabricated content, deciding whether to re-execute, or generating improvement feedback. Activate on "validate output", "check quality", "confidence score", "hallucination check", "should we iterate", "improvement feedback". NOT for executing DAGs (use dag-runtime), planning DAGs (use dag-planner), or matching skills (use dag-skills-matcher).

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Performs claim-evidence verification for agent outputs, recording supported, contradicted, or insufficient-evidence results alongside source accessibility. Activate on 'detect hallucination', 'fact check', 'verify claims', 'check accuracy', 'find fabrications'. NOT for validation (use dag-output-validator) or confidence scoring (use dag-confidence-scorer).

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Validates agent outputs against expected schemas and quality criteria. Reports structural and content checks within the declared evidence scope. Activate on 'validate output', 'output validation', 'schema validation', 'check output', 'output quality'. NOT for confidence scoring (use dag-confidence-scorer) or hallucination detection (use dag-hallucination-detector).

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Select and configure a Coval metric for a concrete product criterion, choosing transcript, audio, trace or deterministic evidence and testing the result. Use for metric creation or scoring design, not for final human calibration.

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Generate competitive SEO content briefs with per-section word counts, competitor scoring, keyword density guidance, and page-type templates. Supports both new page briefs and improve-existing-page briefs. Use when user says "content brief", "write a brief", "content outline", "blog brief", "service page brief", "brief for", "writing brief", "content plan", or "outline for".

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Optimize content for AI Overviews (formerly SGE), ChatGPT web search, Perplexity, and other AI-powered search experiences. Generative Engine Optimization (GEO) analysis including brand mention signals, AI crawler accessibility, llms.txt compliance, passage-level citability scoring, and platform-specific optimization. Use when user says "AI Overviews", "SGE", "GEO", "AI search", "LLM optimization", "Perplexity", "AI citations", "ChatGPT search", or "AI visibility".

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Search Experience Optimization: reads Google SERPs backwards to detect page-type mismatches, derives user stories from search intent signals, and scores pages from multiple persona perspectives. Identifies why well-optimized pages fail to rank by analyzing what Google rewards for each keyword. Use when user says "SXO", "search experience", "page type mismatch", "SERP analysis", "user story", "persona scoring", "why isn't my page ranking", "intent mismatch", or "wireframe".

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Generates creative, research-backed domain name ideas and checks availability with competitor analysis, pattern recognition, and quality scoring. Use when brainstorming brandable domains for a product or project.

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Evaluate design from a UX perspective, assessing visual hierarchy, information architecture, emotional resonance, cognitive load, and overall quality with quantitative scoring, persona-based testing, and actionable feedback. Use when the user asks to review, critique, evaluate, or give feedback on a design or component.

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Interactive review sessions with academic PDFs (lectures, research papers, book chapters). Extract concepts, run Q&A sessions, generate quizzes with scoring. Preserves mathematical formulas in LaTeX format. Privacy-preserving local processing - PDFs never uploaded. Use when studying academic materials, reviewing research, or preparing for exams.

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Instinct-based learning system that observes sessions via hooks, creates atomic instincts with confidence scoring, and evolves them into skills/commands/agents. v2.1 adds project-scoped instincts to prevent cross-project contamination.

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This skill should be used when the user asks to "implement LLM-as-judge", "compare model outputs", "create evaluation rubrics", "mitigate evaluation bias", or mentions direct scoring, pairwise comparison, position bias, evaluation pipelines, or automated quality assessment.

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6 production-ready AI engineering workflows: prompt evaluation (8-dimension scoring), context budget planning, RAG pipeline design, agent security audit (65-point checklist), eval harness building, and product sense coaching.

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Interactive Product Owner skill for requirements gathering, analysis, and PRD generation. Triggers when users request product requirements, feature specification, PRD creation, or need help understanding and documenting project requirements. Uses quality scoring and iterative dialogue to ensure comprehensive requirements before generating professional PRD documents.

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