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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.

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Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.

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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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Build and validate a static DAG reachability index from source-qualified path/chain decompositions and partial transitive-edge filtering. NOT for treating a partial edge filter as a complete transitive reduction or runtime scheduler.

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Design and validate versioned DAGs with typed dependencies, gates, and evidence-bound readiness. NOT for executing a DAG, granting work authority, or treating an unverified gate as cleared.

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Architect data fetching with TanStack Query v5, SWR, optimistic updates, prefetching, and cache invalidation strategies. Activate on: React Query, SWR, optimistic updates, cache invalidation, prefetching, stale-while-revalidate, infinite queries. NOT for: REST API design (use api-architect), database queries (use database skills), GraphQL schema (use graphql-expert).

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Validate finite-DAG order objectives and construct reachability-chain or direct-edge path partitions with explicit proof boundaries. NOT for equating reachability chains with direct-edge paths without checking the chosen objective.

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Validates typed DAG dependency declarations, returns Kahn linear extensions or generations and residual cycle witnesses, and identifies changed consumers for revalidation. NOT for constructing graphs, scheduling resource capacity, granting effects, or executing nodes.

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Designing HTTP cache headers that work correctly across browsers, CDNs, and shared proxies — `Cache-Control` directives per RFC 9111, `stale-while-revalidate` and `stale-if-error` per RFC 5861, the Vary header for varying responses, and surrogate keys for tag-based purging. Grounded in IETF RFCs and Cloudflare/Fastly docs. NOT for service-worker or browser-only caching, Redis/memcached application caching, or edge-function compute.

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Architecture-level decisions for putting a CDN in front of a web app's static assets, API responses, and file/media delivery: provider selection (hyperscaler vs. specialist $/GB), signed-URL / tokenized access for gating private content at the edge, cache invalidation strategy (versioned URLs vs. purge APIs), origin shield / tiered caching for high-miss-rate content, and CDN-layer geo-restriction. Use when deciding which CDN to put in front of a new or growing service, when private/paywalled files need edge delivery without an origin round-trip per request, or when purge/invalidation behavior is being designed rather than debugged. NOT for HTTP cache-control header syntax, Vary, stale-while-revalidate, or surrogate-key purge mechanics (see `cdn-cache-control-headers`); NOT for Cloudflare-specific product configuration once Cloudflare is already chosen (see `cloudflare`); NOT for video-specific transcoding, adaptive bitrate ladders, or streaming-protocol packaging (see `managed-video-streaming-pipeline`).

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Redis caching patterns, cache-aside, write-through, TTL strategies, and invalidation. Activate on: caching, Redis, cache invalidation, cache-aside, write-through, TTL, CDN cache, stale-while-revalidate. NOT for: CDN/reverse proxy setup (use api-gateway-reverse-proxy-expert), database query optimization (use data-warehouse-optimizer).

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Verifies build output integrity after code changes. Runs builds, validates artifact structure, checks for regressions in bundle size, asset references, and static export completeness. The last line of defense before a bad deploy ships.

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Validate one Coval judge against independent human labels, with grouped development/test separation, class-specific errors and uncertainty. Use for trust claims or calibration; without real labels, prepare review rather than inventing ground truth.

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Hreflang and international SEO audit, validation, and generation. Detects common mistakes, validates language/region codes, and generates correct hreflang implementations. Use when user says "hreflang", "i18n SEO", "international SEO", "multi-language", "multi-region", or "language tags".

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Detect, validate, and generate Schema.org structured data. JSON-LD format preferred. Use when user says "schema", "structured data", "rich results", "JSON-LD", or "markup".

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Analyze existing XML sitemaps or generate new ones with industry templates. Validates format, URLs, and structure. Use when user says "sitemap", "generate sitemap", "sitemap issues", or "XML sitemap".

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One-click contribution flow for Open Design (nexu-io/open-design) — even for non-coders. Pick one of four cards (ship a Skill or Design System you made with OD; translate docs; fix a typo / write a blog; report a bug), the agent validates and opens a PR (or issue) for you. Trigger words contribute to open design, ship my OD skill, ship my OD design system, translate OD docs, report an OD bug, od-contribute.

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This skill should be used when the user asks to "PR を出す前に確認して", "check if this branch is ready to merge", "run pre-PR checks", "PRを作る前にチェックして", or wants to verify a branch before opening a pull request. Executes verification commands, validates Conventional Commits format, and confirms documentation is updated, then reports whether gh pr create is safe to run.

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This skill should be used when the user wants to "synthesize two competing solutions without averaging", "resolve a design/value disagreement by lifting to a higher frame", "止揚 / アウフヘーベン", "矛盾を止揚", "独立案を統合", "平均化せず統合", "contradiction lift", "sublate competing designs", or has two good-but-divergent answers to the same question and wants a higher-order resolution (a selection mechanism) or an honest aporia — not a compromise. NOTE: Use this when two independent solutions diverge and you want to PRESERVE both truth-moments while lifting to a higher frame. Use devils-advocate to stress-test ONE proposal with an assigned opponent, strong-inference to find an unknown cause, and dialectic-loop to validate a claim against a real corpus.

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This skill should be used when the user wants to "test a claim against data", "validate an empirical hypothesis", "refine a model/theory with evidence", "characterize a pattern and verify it", "演繹と帰納で検証", "仮説をデータで検証して更新", "実例と反例で確かめる", "弁証法ループ", "主張を現物で裏取り", "傾向分析を検証して精緻化", or mentions iteratively updating a hypothesis by deriving predictions and testing them against a real corpus. NOTE: Use this for VALIDATING/REFINING an empirical claim or model against real data through a derive→test→update loop. Use strong-inference for debugging an UNKNOWN cause, and devils-advocate for adversarially stress-testing a DESIGN proposal.

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This skill should be used when the user wants to "stress-test a design", "challenge an idea", "red team a proposal", "get critical feedback on a design", "validate a design", "adversarial architecture review", "risk assessment", "設計を検証して", "反論をもらいたい", "設計を批判的にレビュー", "デビルズアドボケート", "ストレステスト", "弱点を指摘して", "穴を見つけて", "この設計で良いか", "リスク評価", "設計のアーキテクチャレビュー", or mentions structured adversarial review of a proposal or design. NOTE: Use this for validating PROPOSALS and DESIGNS through adversarial debate, NOT for generic code review, PR review, or normal review requests (use /codex:review or /codex:adversarial-review for those). Also NOT for investigating unknown bugs (use /agent-dialectics:strong-inference for that).

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Create, validate, or clear the optional keel-handoff/v1 pointer override when human intent cannot be inferred uniquely.

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Use when Spark engineering knowledge must be placed, deduplicated, migrated, or validated across AGENTS, Notes, Roles, Skills, and Workflows.

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