Results for “validate”

Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance with Cas-OFFinder/CRISPRitz, ranks them with the published CFD score (SpCas9-only, relative ranker) or MIT/CRISTA/energy models, runs variant-aware screening against gnomAD/individual genomes (CRISPRme), and frames the empirical genome-wide discovery assays (GUIDE-seq, CIRCLE-seq, CHANGE-seq, DISCOVER-seq, Digenome-seq) and high-fidelity nuclease choice (HiFi Cas9, Sniper-Cas9, eSpCas9, SpCas9-HF1). Use when assessing guide RNA specificity, choosing among candidate guides, screening a therapeutic guide against population variation, or planning empirical off-target validation. Distinguishes predicted vs detected vs validated. On-target activity scoring and deaminase (Cas-independent) base/prime-editor off-targets are separate skills.

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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.

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Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS, JointPRS, PRSmix, or PGS Catalog Calculator with ancestry-aware reference panels (HapMap3, UKB-LD), Pejaver-style calibration, and PRS-RS reporting standards. Use when computing PRS for cohorts, applying Whiffin-style absolute-risk transformation, assessing cross-ancestry portability (Martin 2017 / Ding 2023 continuous ancestry), or auditing PRS manuscripts against the 22-item PRS-RS reviewer checklist.

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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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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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Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and pose-energy reasonableness. Filters AI-docking outputs (DiffDock, EquiBind, NeuralPLexer) where ~50% of poses fail physical-validity tests. Use when QC-ing docking results, comparing classical vs ML docking outputs, or filtering pose lists before SAR analysis.

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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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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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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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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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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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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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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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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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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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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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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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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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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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