「va」の検索結果

Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation direction. Use when a study centers on process-related genes, DEG and WGCNA integration, machine-learning feature selection, nomogram-based diagnostic modeling, immune infiltration, regulatory-network analysis, and optional external or experimental validation. Covers five study patterns (process-DEG discovery, co-expression-module integration, machine-learning biomarker selection, diagnostic model/nomogram workflow, immune-regulatory interpretation and validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

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Extends a mechanistic or association-level biomedical finding into a staged validation pathway that moves from descriptive evidence toward stronger functional support, mechanistic specificity, and clinical relevance. Use this skill when a user has a pathway, biomarker, cell-state, target, mechanism, or association finding and needs to decide what should be validated next, in what order, and which evidence layers are necessary versus optional. Do not default to maximal validation stacks. Build a structured validation ladder with a primary route, stronger upgrade route, and optional extensions.

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Generates complete conventional non-oncology bioinformatics research designs from a user-provided disease context, process-related gene family or biological theme, and validation direction. Use when a study centers on multi-dataset bulk transcriptome integration, DEG analysis, process-gene intersection, enrichment analysis, GSEA, PPI hub-gene prioritization, TF/miRNA regulatory networks, ROC-based biomarker evaluation, and immune infiltration analysis. Covers five study patterns (process-DEG discovery, enrichment/GSEA interpretation, hub-gene prioritization, regulatory-network and immune interpretation, multi-layer public validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

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Use when running prognostic survival analysis on a clinical cohort with time-to-event data to estimate univariate and multivariable Cox proportional hazards models, export result tables, and generate forest plots. NOT for: nomogram construction, calibration curves, time-dependent ROC analysis, or model training/feature selection beyond the built-in univariate screening rule.

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Migrate Java EE javax.* imports to Jakarta EE jakarta.* namespace. Use when upgrading to Spring Boot 3.x, migrating javax.persistence, javax.validation, javax.servlet imports, or fixing compilation errors after Jakarta EE transition. Covers package mappings, batch sed commands, and verification steps.

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Maintenance orchestrator for the brooks-lint plugin itself. Runs a sequential subagent pipeline — author → eval → QA → trigger-audit → release — to add or edit a skill, refresh the eval suite, keep the four manifests + all README translations + CHANGELOG + AGENTS/GEMINI in sync, audit trigger boundaries, and cut releases. Drives the five agents in .claude/agents/ (skill-author, eval-curator, consistency-qa, trigger-boundary-auditor, release-manager). Triggers when the maintainer asks to work ON brooks-lint itself: "add a new skill", "edit the brooks-debt guide", "update the eval suite", "fix the trigger descriptions", "make this change and validate it", "release brooks-lint", "bump and publish", and follow-ups: "re-run", "re-validate", "update that skill", "redo the audit", "do the X part again". Do NOT trigger for: USING the brooks-lint analysis skills on some target codebase (that's brooks-review / brooks-audit / brooks-debt / brooks-test / brooks-health / brooks-sweep); generic questions about brooks-lint that don't ask to change it; or maintenance of a different plugin.

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Calibrate an LLM judge against human labels using data splits, TPR/TNR, and bias correction. Use after writing a judge prompt (write-judge-prompt) when you need to verify alignment before trusting its outputs. Do NOT use for code-based evaluators (those are deterministic; test with unit tests per `write-code-eval`).

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Design an evaluation plan for an LLM or AI feature before shipping it. Use when asked how to evaluate a prompt/model/agent, set up an eval harness, define quality metrics for an AI feature, or build a regression gate. Produces an eval plan — task definition, datasets, metrics & rubrics, baselines, automated + human evals, a pass bar, and a regression gate.

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Evaluates LLMs across 60+ academic benchmarks (MMLU, HumanEval, GSM8K, TruthfulQA, HellaSwag). Use when benchmarking model quality, comparing models, reporting academic results, or tracking training progress. Industry standard used by EleutherAI, HuggingFace, and major labs. Supports HuggingFace, vLLM, APIs.

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Use when packaging ACM CCS artifacts for the artifact-evaluation committee and the ACM badges — Artifacts Available, Artifacts Evaluated Functional, Artifacts Evaluated Reusable, and Results Reproduced — covering what security evaluators inspect, how to make attacks and defenses turnkey, and how to justify withheld artifacts.

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Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.

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Estimates tumor fraction (the genome-wide proportion of cfDNA molecules that are tumor-derived, the cfDNA analogue of bulk-tumor purity) from shallow whole-genome sequencing with ichorCNA, an HMM over 1 Mb bins that jointly EM-estimates tumor fraction, ploidy, and subclonal prevalence over a normal/ploidy grid. Encodes the load-bearing reframes: tumor fraction is the quantity that travels across assays and is NOT mutation VAF (clonal-het VAF approximately TF/2), CNA-based estimation has a hard ~3 percent limit-of-detection floor, and near-diploid or copy-neutral-LOH genomes return a falsely low value. Selects the estimator by data type (sWGS to ichorCNA, deep panel to max-VAF, methylation to deconvolution, sub-3 percent to fragmentomics or methylation). Use when quantifying tumor burden from a liquid biopsy, picking a tumor-fraction estimator for a given assay, or reconciling a TF estimate against a panel VAF.

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Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired MANDATORILY with PERMDISP (Anderson & Walsh 2013; dispersion confounds centroid tests), Joint Species Distribution Models (HMSC, sjSDM, gjam) with explicit rejection of "residual covariance equals biotic interaction", phylogenetic community ecology (SES_MPD/MNTD), trait-environment via RLQ + fourth-corner with corrected modeltype=6 (Dray 2014), bipartite network metrics (NODF, modularity) with curveball null (Strona 2014), and Mantel-test replacements (dbRDA, GDM) for spatial data. Use when testing how environmental gradients structure communities, identifying habitat indicator taxa, partitioning variance among predictors, deciding whether PERMANOVA significance is location vs dispersion, picking among HMSC/sjSDM/gjam, or replacing Mantel tests for landscape data.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Increase widget visibility on Apple Watch using RelevanceKit. Use when providing contextual relevance signals for watchOS widgets, declaring time-based or location-based relevance, combining multiple relevance providers, helping the system surface the right widget at the right time on watchOS 26, or routing mixed RelevanceKit/WidgetKit/HealthKit/MapKit Smart Stack scope.

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Set up worker environment and per-worker state for parallel pools. Use when code needs paths, environment variables, database connections, loaded libraries, or expensive objects available on workers before parfor/parfeval runs. Teaches parallel.pool.Constant, parfevalOnAll, and parpool name-value pairs. Also use when refactoring existing code that uses spmd for side-effect setup (an anti-pattern). Triggers: worker setup, pool constant, per-worker state, non-serializable, loadlibrary on workers, database connection parfor, addpath workers, spmd before parfor, worker environment, reduce parfor overhead, parfor setup, resource creation in parallel loop, cannot serialize error, undefined function or variable on workers error, load data per worker, reduce data transfer, parallelize setup, improve parallel code.

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Prepare a Neva GitHub release draft from merged PRs, previous release style, and local multi-platform artifacts. Use this for monthly release preparation in nevalang/neva.

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Convert Neva programs to valid Mermaid flowchart diagrams. Use when asked to visualize Neva code as Mermaid.

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Configure the Canvas Authoring MCP server for the current coauthoring session. USE WHEN "configure MCP", "set up MCP server", "MCP not working", "connect Canvas Apps MCP", "canvas-authoring not available", "MCP not configured", "set up canvas apps".

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Cross-format content adaptation. Turning one substantial piece into many derivative formats (blog series, email sequences, social posts, webinars, podcasts, video shorts) without losing the original's value or producing AI-slop variants. The discipline of adaptation per medium rather than mass-blast distribution. Triggers on content repurposing, content adaptation, cross-format content, content atomization, content multiplication, content distribution across formats, source-piece-to-derivative, video shorts from blog, email from whitepaper, podcast from article, blog series from research. Also triggers when a flagship piece is shipping but the team has not planned how to extend it across formats, when repurposing is happening but the derivatives feel mass-produced, or when AI-assisted repurposing is producing slop variants of strong source pieces.

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Expert ISO 27701 Privacy Information Management System (PIMS) compliance advisor. Use this skill whenever a user asks about ISO/IEC 27701:2025, ISO/IEC 27701:2019, privacy information management, PIMS certification, PII controller or processor obligations, privacy risk assessment, Statement of Applicability for privacy, privacy by design, data subject rights, DPIA, records of processing activities, transitioning from ISO 27701:2019, GDPR alignment with ISO 27701, or any privacy management system topic. Also trigger for questions about Annex A.1 (controller controls), A.2 (processor controls), A.3 (shared security controls), or implementing a standalone PIMS without ISO 27001. When in doubt, use this skill — it covers the full ISO 27701 lifecycle from gap assessment through certification.

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Build custom LLM evaluation pipelines using the OpenJudge framework. Covers selecting and configuring graders (LLM-based, function-based, agentic), running batch evaluations with GradingRunner, combining scores with aggregators, applying evaluation strategies (voting, average), auto-generating graders from data, and analyzing results (pairwise win rates, statistics, validation metrics). Use when the user wants to evaluate LLM outputs, compare multiple models, design scoring criteria, or build an automated evaluation system.

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Use when the user has run multiple evaluation skills and wants a comprehensive analysis — maturity assessment, cross-skill signals, trends, prioritized actions, and an executive summary. Also use when the user mentions eval health check, evaluation audit, ship readiness, evaluation maturity, or "how good is my evaluation system itself." This is a read-only analysis skill.

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A zero-hallucination privacy-policy generator that takes anyone — non-lawyer founder to lawyer — from a guided intake to a publishable, jurisdiction-aware privacy policy. Jurisdiction-first: it detects which laws apply from where your users are, then drafts only the required clauses — GDPR/EU + UK, US (CCPA/CPRA, ~20 state laws, COPPA, sector overlays), and global/MENA (LGPD, Quebec Law 25, India DPDP, China PIPL, UAE/DIFC, Saudi PDPL), plus app-store, cookies, and AI/EU AI Act disclosures. Its rule: state only what you confirm; never invent a statute, citation, fine, or date — every claim is source-cited and QA-gated. Not legal advice.

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