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Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models, compositional (Dirichlet/scCODA) differential abundance, diffcyt, per-image-to-patient spatial differential testing (SpaceANOVA), batch covariates, and FDR. Use when testing whether a cell type or spatial niche differs between groups, avoiding cell-level pseudoreplication, choosing a differential-abundance method, or correctly powering an IMC cohort comparison.

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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.

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Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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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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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Use this skill when the user asks the cost of pulling a Motor Vehicle Record (MVR) in a specific state, or wants to compare MVR fees across multiple states, or is budgeting annual compliance costs for a multi-state fleet. Reference the canonical fee table below; flag that fees change (re-verify with state DMV before annual budget planning).

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Use this skill to evaluate which defensive driving program is best for your fleet. Compares Smith System, CarriersEdge, Compass-native training, and other options.

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Debugs recorded DAG lineage through historical inspection, deterministic decision replay when prerequisites hold, and clearly labeled counterfactual or live re-execution. Activate on "debug DAG", "replay execution", "inspect node state", "compare runs", or "execution diff". NOT for live monitoring (use dag-runtime + websocket-streaming), failure analysis (use dag-ops), or general code debugging.

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Choose, compare, and decompose work into the right coordination topology: dag, workflow, manager-driven team, swarm, blackboard, team-builder, or recurring loop. Use when the coordination shape is unclear, when you need topology-native breakdown instructions instead of a generic DAG, or when planning topology and runtime topology may differ. NOT for actual execution, node-level skill matching, or framework/tool installation.

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Data structures and serialization formats for agent-to-agent communication. Covers message envelopes, structured output schemas, capability declarations, task handoff payloads, error/retry signaling, and context windows as data structures. Compares the version-pinned A2A, MCP, and JSON-RPC role boundaries covered by this bundle; OpenAI and LangChain-specific APIs require their own current sources. Teaches when to use rigid schemas versus free-form content with validation, typed versus untyped boundaries, and streaming versus batch. Activate on: "agent message format", "agent communication schema", "agent-to-agent protocol", "A2A protocol", "MCP message format", "structured output for agents", "agent interop", "interchange format", "agent serialization", "task handoff format", "capability declaration". NOT for: what agents say to each other (use agent-conversation-protocols), orchestration topology (use multi-agent-coordination), building agent infrastructure (use agentic-infrastructure-2026).

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Generate SEO-optimized competitor comparison and alternatives pages. Covers "X vs Y" layouts, "alternatives to X" pages, feature matrices, schema markup, and conversion optimization. Use when user says "comparison page", "vs page", "alternatives page", "competitor comparison", "X vs Y", "versus", "compare competitors", or "alternative to".

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SEO drift monitoring: capture baselines of SEO-critical elements, detect changes, and track regressions over time. Git for SEO: baseline, diff, and track changes to your on-page SEO. Use when user says "SEO drift", "baseline", "track changes", "did anything break", "SEO regression", "compare SEO", "before and after", "monitor SEO changes", or "deployment check".

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Orchestrator that runs one UI brief through all four ui-* posture skills in parallel, then picks and merges a winner. Use when a screen matters enough to explore several directions, or the user says 'build it a few ways', 'design options', 'bake-off', 'show me variations', or 'compare approaches'.

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Search domains, compare prices, find promo codes, get purchase recommendations. Use when user wants to buy a domain, check prices, or find domain deals.

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Enables Claude Code to collaborate with OpenAI Codex CLI on Windows. Use this skill when the user wants to get a second opinion from Codex, compare approaches between Claude and Codex, or leverage both AI assistants for collaborative problem-solving. This skill supports both non-interactive mode (automatic response retrieval) and interactive mode (visual pane splitting with tmux).

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Researches a question to something usable — a verdict with a flip condition, a versioned playbook or a graded report — every claim tagged by evidence. Trigger on which X should I pick (even from pasted pages), is Y worth it, compare A vs B, go/no-go, research this, deep research, fact-check a doc, write or merge a reference guide or playbook, grade a research report, read a bot-blocking source (Reddit, YouTube, X), or map an unfamiliar repo before contributing (entry points, flows, where to change X); or say researchscribe (verdict, playbook, research, verify, sources, map, refresh). Code review is engineering tooling's; fiction canon is lorescribe's; messages commscribe's; prompt model picks promptwright's; skill niches skillwright's; config rigwright's; brands brandscribe's.

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Finds what changed in Claude — docs, release notes, changelogs, GitHub and community posts on Claude Code, claude.ai, Cowork, the API and models — and turns each change into adopt rows for your setup, plus a fit card for a new model or feature and a monthly bench of your skills against public skill and plugin repos (build, adopt or skip). Trigger on what changed since a date or version, a weekly sweep, features worth adopting, a feature that broke unannounced, a stale model table, what a new model or feature is good for, or how your skills compare with popular or little-known skill and plugin repos; or say scoutwright (sweep, since, watch, adopt, fit, bench, sources, refresh). Outside research is researchscribe's; applying a row, skillwright's; config, rigwright's; schedules, agentwright's; tier picks, promptwright's.

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[22] UNDERSTAND. Deep research from all sources — internal (code, git, logs) AND external (web, docs, best practices). Use when choosing libraries, investigating solutions, understanding legal/technical questions, comparing approaches, or anytime you need comprehensive knowledge from both project context and world knowledge. Triggers on "research", "investigate", "find best approach", "what do others do", "compare options", or complex questions requiring multiple sources.

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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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Acts as a professional UX/UI specialist. Use to analyze web/app design, compare solutions, and identify potential UX problems. Provides expert advice on usability and accessibility for users with disabilities, including visual impairments.

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Research markets with sizing, segmentation, competitor mapping, pricing checks, and demand validation that turn fuzzy ideas into decision-ready evidence. Use when (1) you need TAM, SAM, SOM, whitespace, or category sizing; (2) you must compare competitors, pricing, positioning, or customer segments before acting; (3) the user asks whether a niche, launch, expansion, or go-to-market bet is actually worth pursuing.

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Compare cross-border e-commerce shipping options, packaging tactics, customs-risk signals, and speed-versus-cost tradeoffs for sellers, operations teams, and marketplace operators. Use when choosing routes, carriers, declaration practices, or packaging plans for parcel shipments without relying on live carrier APIs.

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Backtest crypto and traditional trading strategies against historical data. Calculates performance metrics (Sharpe, Sortino, max drawdown), generates equity curves, and optimizes strategy parameters. Use when user wants to test a trading strategy, validate signals, or compare approaches. Trigger with phrases like "backtest strategy", "test trading strategy", "historical performance", "simulate trades", "optimize parameters", or "validate signals".

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