'annotation' 검색 결과

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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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

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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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Quantitative agent evaluation using 4-metric framework (correctness/step_ratio/tool_call_ratio/latency_ratio) with ideal trajectory annotation and capability-categorical taxonomy. Use when measuring agent efficiency, comparing agent variants, or gating new agents through correctness→efficiency phases. Complements harness-eval (SE benchmarks) and evaluator-optimizer (qualitative rubric).

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Report the health of the central system spec at `docs/system/` across seven checks — coverage gaps, stale elements, dangling anchors, duplicate anchors, orphan shards, unillustrated elements, and shards missing their kind annotation. Report-first and read-only: it repairs nothing until a human confirms a specific item. Use when the corpus has drifted, after a merge that touched `docs/system/`, or from `/archive` Step 5.5 in report-only mode. Requires `memory.architecture_map.enabled`.

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Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.

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Use when creating a new Laravel API endpoint — Controller, FormRequest, Resource, route, Policy, OpenAPI annotations — versioned route layout, single-action `__invoke` controllers.

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Transforms data into compelling visual narratives by applying narrative structure, annotation techniques, scrollytelling patterns, and honest framing to data journalism, presentations, and infographics. Use when creating data-driven articles or reports, designing infographics with narrative, building scrollytelling experiences, annotating charts to guide interpretation, or when user mentions data storytelling, presentation design, annotated chart, narrative visualization.

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NYT-discipline data visualization. Applies the design rules of The New York Times graphics desk + Upshot — color, typography, annotation, chart-type selection — to make any chart render at Times grade. Use whenever generating charts, dashboards, reports, or data-driven webpages. Triggers: "make this chart look professional", "NYT style", "editorial chart", "data viz", "dashboard design".

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Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.

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Recast a supplied everyday photo as a witty illustrated product instruction sheet with a large Chinese title and concise English annotations. Use for 日常说明书、宠物使用说明、生活物品冷幽默说明图 or a fictional everyday object manual poster.

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Register WordPress Abilities: machine-readable plugin operations with JSON Schema contracts, required permission callbacks, optional REST exposure, and AI/MCP-friendly discovery. Covers categories, wp_register_ability, WP_Ability::execute, REST run endpoints, meta.show_in_rest, annotations, and Ability vs REST route vs custom hook decisions. Use when exposing plugin functionality to agents, admin JS, external tools, or reviewing AI integration code.

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Read the latest Glassbox code review and apply all feedback annotations

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Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.

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Enable nullable reference types in a C# project and systematically resolve all warnings. USE FOR: adopting NRTs in existing codebases, file-by-file or project-wide migration, fixing CS8602/CS8618/CS86xx warnings, annotating APIs for nullability, cleaning up null-forgiving operators, upgrading dependencies with new nullable annotations. DO NOT USE FOR: projects already fully migrated with zero warnings (unless auditing suppressions), fixing a handful of nullable warnings in code that already has NRTs enabled, suppressing warnings without fixing them, C# 7.3 or earlier projects. INVOKES: Get-NullableReadiness.ps1 scanner script.

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Make .NET projects compatible with Native AOT and trimming by systematically resolving IL trim/AOT analyzer warnings. USE FOR: making projects AOT-compatible, fixing trimming warnings, resolving IL warnings (IL2026, IL2070, IL2067, IL2072, IL3050), adding DynamicallyAccessedMembers annotations, enabling IsAotCompatible. DO NOT USE FOR: publishing native AOT binaries, optimizing binary size, replacing reflection-heavy libraries with alternatives. INVOKES: no tools — pure knowledge skill.

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Bootstrap an AI-agent skill from a TypeScript codebase by running the deterministic skillit generate/audit loop and enriching repo source (JSDoc, README, config-type properties, MCP tool annotations, examples, package.json) until the skill reaches its grade target. Use for cli, typedoc, config, or mcp (build-mode) projects; never edit SKILL.md/references directly.

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MCP server documentation conventions for high-quality generated skills. Use when writing tool descriptions, `_meta` annotations, or input schemas for MCP extraction.

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Add redaction annotations to sensitive fields in schemas to block or hash PII. Use when configuring GDPR/HIPAA compliance, protecting credentials, or blocking internal fields from materializations. Use when user says "protect PII", "hide sensitive data", "hash field", "redact field", "GDPR compliance", "don't capture field", "remove field from Estuary", or "prevent Estuary from capturing field".

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Create an Estuary derivation that continuously aggregates metrics (daily totals, running counts, min/max, lifetime revenue) using reduction annotations. Use for real-time dashboards, continuous materialised views, and replacing batch ETL aggregations with streaming. Derivations add complexity and cost — confirm the user wants a derivation before reaching for this. Use when user says "aggregation derivation", "derivation to sum daily totals", "running-count derivation", "transformation for min/max per group", "derive lifetime metrics", "aggregate-by-date derivation", or "real-time-dashboard derivation".

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Use when working with Buildkite — buildkite CI/CD pipeline and agent management. Covers build pipeline status, agent pool health, artifact management, build annotations, and cluster queue monitoring. Use when checking build status, investigating failures, managing agents, or reviewing pipeline configurations.

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Use when working with Aws Xray — aWS X-Ray trace analysis, service map generation, fault and error analysis, sampling rule management, and latency investigation. Covers trace summaries, segment analysis, annotation-based filtering, and group configuration.

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Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks.

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Build a throwaway prototype to answer a design question, as UI variations or a state-model walkthrough. Use when the user types /prototype, wants to sanity-check whether a state model or logic feels right, wants to explore what a UI should look like, or as the prototype step of the web design flow with brainstorm or grill before the final plan goes to plan-canvas (annotate the running prototype with the plan-canvas annotation tool).

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