'testing' 검색 결과

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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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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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.

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Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, mixed), Hochberg/Hommel/Holm with PRDS, and the closed-testing principle (Marcus-Peritz-Gabriel; Goeman 2021 admissibility). Covers FDA Multiple Endpoints Final Guidance (October 2022), graphical procedures via R gMCP, primary + key-secondary + subgroup hierarchies, and FWER vs FDR distinction. Use when designing the multiplicity strategy for confirmatory trials with multiple primary or key secondary endpoints.

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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

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Use when a driver has been involved in a crash — regardless of preventability or injury — and the carrier needs to handle the immediate, post-investigation, and return-to-work phases. Covers trauma response, post-accident testing under 49 CFR 382.303, paid time off, retraining, light duty, and re-entry planning.

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Use this skill when selecting a Consortium/Third-Party Administrator (C/TPA) for drug + alcohol testing program management. Covers what services they provide, what to look for, and red flags.

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Use this skill when an owner-operator (single CDL driver, single operating authority) needs to comply with random testing. Covers consortium membership, pool size requirements, and self-employed driver rules.

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Use this skill when hiring a driver who has a recent valid pre-employment test from a prior employer. Covers the conditions under § 382.301(c) that allow accepting it instead of testing again.

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Use this skill when the user asks about onboarding a new CDL driver — pre-hire process, day-zero requirements, application + DQF setup, road test, drug & alcohol pre-employment, Clearinghouse Full query, MVR initial pull, PSP report, ELDT verification, sequence of activities + timing, and what NOT to do (handing keys before testing complete). Cite 49 CFR 391, 382.

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Use this skill when referring a driver to SAP after a positive test or refusal. Covers SAP selection, the evaluation/treatment cycle, return-to-duty test, and follow-up testing schedule.

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Use this skill when selecting an MRO for drug testing program oversight. Covers MRO qualifications under Part 40, what the MRO does, and how to evaluate MRO services.

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Use this skill when the user asks about accident registers, DOT-recordable accident definitions, what counts as a "reportable accident" under 49 CFR 390.5 + 390.15, accident register retention, post-accident testing trigger logic, FMCSA accident reporting (no longer required to FMCSA directly for non-fatal accidents), insurance reporting timelines, and what to do after a CMV crash. Cite 49 CFR 390.5 + 390.15.

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Create and review Cloudflare Durable Objects. Use when building stateful coordination (chat rooms, multiplayer games, booking systems), implementing RPC methods, SQLite storage, alarms, WebSockets, or reviewing DO code for best practices. Covers Workers integration, wrangler config, and testing with Vitest. Biases towards retrieval from Cloudflare docs over pre-trained knowledge.

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Refute-before-prove research discipline: automated counterexample sweeps before any formalization, meter-integrity audits for information-bound experiments, mutation-tested model checkers, pre-registered commit-or-cut gates for speculative directions, wrong-turn reporting, and numeric-claim provenance. Use when validating any new theorem, bound, equilibrium, or security claim; when building or trusting a checker, simulator, or experiment; or when deciding whether a speculative research direction lives or dies. NOT for exploratory brainstorming, product prioritization, writing style, or literature review.

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Rigorous benchmarking of multi-agent coordination systems: experiment design, statistical analysis, human evaluation protocols, and reproducible reporting. NOT FOR ML model evaluation (use llm-evaluation-harness), A/B testing for web products, survey design, or general data science.

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dbt Core/Cloud data transformations, testing, documentation, and CI/CD. Activate on: dbt, data transformation, analytics engineering, ref, source, staging model, mart, dbt test. NOT for: orchestration/scheduling (use airflow-dag-orchestrator), data warehouse tuning (use data-warehouse-optimizer).

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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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Expert in developer tool documentation as a product. Activate on: docs site, getting started guide, API reference, developer documentation, Docusaurus, Mintlify, Nextra, ReadMe, migration guide, troubleshooting page, docs information architecture, documentation testing, llms.txt. NOT for: marketing copy (use seo-content-blogging), API design itself (use api-architect), general technical writing (use technical-writer).

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Design modern, intuitive DAG/workflow visual editors that feel like LEGO, not LabView NOT for runtime DAG admission, graph execution, or claiming usability without user testing.

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