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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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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer canonicalization, stereochemistry standardization, mixture handling, and isotope normalization. Explicitly compares ChEMBL pipeline, canSARchem, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Use when a carrier asks which KPIs to track, how to build a fleet dashboard, what targets to set, cadence for reviewing metrics (daily / weekly / monthly / quarterly), and how to operationalize data into actions. Covers safety, operations, financial, driver, and customer KPIs.

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Use when a carrier asks about fuel-card vendor selection (Comdata, EFS, WEX, RTS, Pilot Flying J, Love's Connect), discount levels, fraud control, driver authorization PINs, IFTA reporting features, cash advance, money codes, or how the card fits into payroll/settlement workflows.

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Use this skill when the user asks about Electronic Logging Device (ELD) compliance under 49 CFR 395.20-38 — ELD mandate, AOBRD vs ELD transition, ELD exemptions, ELD malfunctions, 8-day paper backup, ELD certification on FMCSA registered list, data file integrity, edits + annotations, driver portability, and how to handle ELD failures at roadside. Cite 49 CFR 395.20-395.38.

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Use this skill when a crash has been incorrectly classified as DOT-recordable when it shouldn't be. Covers the § 390.5 criteria, common misclassifications, and challenge process.

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Use this skill to understand what CSA data the public sees about your carrier and how that affects business. Covers SAFER, accessibility, and what's hidden vs visible.

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Use this skill when the user asks about FMCSA Compliance Safety Accountability (CSA) program scoring — the seven BASIC categories, BASIC Severity Indicator (BSI), peer percentiles, intervention thresholds, how violations age out, SMS Methodology, ISS (Inspection Selection System), what "alert" status means, Safety Measurement System mechanics, or DataQ disputes. Cite SMS Methodology v3.20.

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Use this skill when the user asks how to investigate a CMV accident — what to do at the scene, the first 24 hours, evidence preservation, who to call, preventability determination, ELD data preservation, dash cam review, witness interviews, working with insurance + attorney, and how to build a learning culture from incidents. Reference 49 CFR 392.7 + insurance industry best practices.

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Use this skill to explain to customers/sales prospects why FMCSA CSA scores are not available in real-time. Covers the SAFER refresh cycle and what 'real-time' actually means for CSA data.

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Rigorous benchmarking of multi-agent coordination systems: experiment design, statistical analysis, human evaluation protocols, and reproducible reporting. NOT FOR ML model evaluation (use llm-evaluation-harness), A/B testing for web products, survey design, or general data science.

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Data structures and algorithms for AI agent episodic memory. Covers vector stores (HNSW, IVF, PQ), temporal indexing, knowledge graphs with triple stores, hierarchical summarization, forgetting curves, working/long-term/ procedural memory, and memory consolidation. Deep analysis of MemGPT/Letta, Zep/Graphiti, Mem0, and the Stanford generative agents memory architecture. Teaches the CS fundamentals behind how agents remember, retrieve, and forget. Activate on: "agent memory", "episodic memory", "vector search algorithm", "HNSW", "memory retrieval", "forgetting curve", "knowledge graph memory", "MemGPT", "Letta", "Zep", "Mem0", "memory consolidation", "temporal retrieval", "agent long-term memory", "memory layer". NOT for: conversation protocol design (use agent-conversation-protocols), agent infrastructure selection (use agentic-infrastructure-2026), building RAG pipelines (use ai-engineer).

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Flutter state management expert with BLoC/Cubit, Riverpod, Provider, and Navigation 2.0 (GoRouter). Activate on: Flutter state management, BLoC pattern, Cubit, Riverpod, Provider, GetX, GoRouter, Flutter navigation, flutter_bloc. NOT for: React Native (use react-native-architect), SwiftUI (use swiftui-data-flow-expert), Jetpack Compose (use jetpack-compose-navigation-expert).

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Use for sensemaking, frame revision, anomaly handling, questioning strategy, and ambiguity diagnosis with the Data/Frame model before action is chosen. NOT for deterministic classification, settled execution planning, or situations where the frame is already stable.

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Advanced CV for infrastructure inspection including forest fire detection, wildfire precondition assessment, roof inspection, hail damage analysis, thermal imaging, and 3D Gaussian Splatting reconstruction. Expert in multi-modal detection, insurance risk modeling, and reinsurance data pipelines. Activate on "fire detection", "wildfire risk", "roof inspection", "hail damage", "thermal analysis", "Gaussian Splatting", "3DGS", "insurance inspection", "defensible space", "property assessment", "catastrophe modeling", "NDVI", "fuel load". NOT for general drone flight control, SLAM, path planning, or sensor fusion (use drone-cv-expert), GPU shader development (use metal-shader-expert), or generic object detection without inspection context (use clip-aware-embeddings).

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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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