Results for “tests”

Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.

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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submissions or precision-medicine claims.

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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Great Expectations, dbt tests, anomaly detection, and data contracts for data quality. Activate on: data quality, data validation, Great Expectations, data contract, anomaly detection, SLA, freshness check, schema validation. NOT for: dbt model structure (use dbt-analytics-engineer), schema evolution (use schema-evolution-manager).

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Interprets GitHub Actions run status and logs, diagnoses CI failure patterns, and suggests targeted fixes. Handles dependency install failures, test timeouts, build OOM, flaky tests, and workflow misconfigurations. Activate on: 'CI failing', 'build broken', 'workflow error', 'GitHub Actions debug', 'flaky CI', 'pipeline timeout', 'CI red'. NOT for: writing new workflows from scratch (use github-actions-pipeline-builder), CI caching strategy (use ci-cache-optimizer), deployment orchestration (use devops-automator).

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Safety-case design for always-on agents with episodic memory. Covers data hygiene, privacy and security risk surfaces, cost controls, scope, user dependency concerns, retention, incident containment, and responsible deployment evidence. It identifies hazards and asks for named controls, tests, owners, and residual uncertainty; it does not provide legal, clinical, youth-safety, or jurisdictional determinations. Activate on: "agent safety", "always-on agent privacy", "agent cost control", "persistent agent risks", "AI companion safety", "agent data hygiene", "runaway agent costs", "parasocial AI risk", "/always-on-agent-safety". NOT for: architecture design (use always-on-agent-architecture), input design (use always-on-agent-inputs), application brainstorming (use always-on-agent-applications), healthcare compliance specifically (use hipaa-compliance).

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Build voice AI agents with LiveKit Cloud and the Agents SDK. Use when the user asks to "build a voice agent", "create a LiveKit agent", "add voice AI", "implement handoffs", "structure agent workflows", or is working with LiveKit Agents SDK. Provides opinionated guidance for the recommended path: LiveKit Cloud + LiveKit Inference. REQUIRES writing tests for all implementations.

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Debug Keel agent command or validation failures under Keel's selected OpenSpec task contract. Use when `/opsx:apply` or a selected task reports failed commands, failing tests, validation errors, stop decisions, or needs an evidence-bound failure report.

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Drive Keel agent test-first or evidence-first execution for a selected OpenSpec task. Use when a task needs software tests, hardware testbench, assertions, lint, new behavior proof, regression coverage, or red/green evidence before implementation.

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Use when adding or repairing Spark regression tests for asynchronous ownership, cancellation, persistence, restart recovery, or cross-surface projections. Not a coverage campaign, performance benchmark, source-text policy check, or full delivery review.

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Generate convex-test tests for the app's Convex functions.

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Use when adding or repairing Spark regression tests for asynchronous ownership, cancellation, persistence, restart recovery, or cross-surface projections. Not a coverage campaign, performance benchmark, source-text policy check, or full delivery review.

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Generates State pattern for PHP 8.5. Creates state machines with context, state interface, and concrete states for behavior changes. Includes unit tests.

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Generates PSR-20 Clock implementation for PHP 8.5. Creates ClockInterface implementations including SystemClock, FrozenClock, and OffsetClock for time abstraction and testing. Includes unit tests.

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Generates DDD Value Objects for PHP 8.5. Creates immutable, self-validating objects with equality comparison. Includes unit tests.

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Generates Strategy pattern for PHP 8.5. Creates interchangeable algorithm families with context class, strategy interface, and concrete implementations. Includes unit tests.

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Generates CQRS Queries and Handlers for PHP 8.5. Creates read-only query DTOs with handlers that return data without side effects. Includes unit tests.

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Generates DDD Specification for PHP 8.5. Creates reusable business rule objects for validation, filtering, and querying with composite pattern support. Includes unit tests.

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Guide for writing high-quality acceptance criteria and acceptance tests using industry-standard BDD (Behavior-Driven Development) and ATDD (Acceptance Test-Driven Development) practices. Use this skill when creating acceptance criteria for user stories, writing Gherkin scenarios, or implementing acceptance test specifications following Given-When-Then format.

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