测试与安全技能

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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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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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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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

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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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Manage BAP (Bitcoin Attestation Protocol) identity files using bap-cli. This skill should be used when users need to create, decrypt, list, or extract BAP identity backups, work with .bep encrypted files, or generate test fixtures for Playwright tests involving BAP identities.

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Master Bash Automated Testing System (Bats) for comprehensive shell script testing. Use when writing tests for shell scripts, CI/CD pipelines, or requiring test-driven development of shell utilities.

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Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.

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Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "beat the baseline on this benchmark", "run a search over approaches and keep the best", "do an MLE-bench / Kaggle-style optimization", or any long-horizon "make this artifact better and don't just memorize the dev set" task. Trigger it even when the user doesn't say "Arbor" or "hypothesis tree" but describes repeated experiment-and-evaluate loops, branching exploration of competing ideas, or worries about a dev/test gap. Runs Claude itself as the coordinator with subagent executors in isolated git worktrees; for the standalone `arbor` CLI tool see references/arbor-upstream.md.

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Testing patterns for PHPUnit and Playwright E2E tests. Use when writing tests, debugging test failures, setting up test coverage, or implementing test patterns for ActivityPub features.

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Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include "method validation", "analytical method validation", "AMV", "validation protocol", "acceptance criteria", "linearity", "reportable range", "accuracy and precision", "repeatability", "intermediate precision", "recovery", "LOD", "LOQ", "detection limit", "quantitation limit", "specificity", "robustness", "method transfer", "method comparison", "Deming", "Passing-Bablok", "Bland-Altman", "equivalence testing", "OOS investigation", "ICH Q2", "Q2(R2)", "Q14", "USP 1225", "ICH M10", "incurred sample reanalysis", "ISR", "CLSI EP", and any request to show that an assay works.

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Генерация полных Python pytest тестов для REST API эндпоинтов с валидацией схемы. Использовать при создании тестов для новых эндпоинтов, добавлении покрытия для CRUD операций или валидации соответствия API с OpenAPI схемами.

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Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test web pages. Use whenever a browser would be useful, not just when the user explicitly asks.

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Master authentication and authorization patterns including JWT, OAuth2, session management, and RBAC to build secure, scalable access control systems. Use when implementing auth systems, securing APIs, or debugging security issues.

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Read-only audit of the project's agent-tree structural overhead vs the context window. NOT for cost tracking (budget skill); NOT for read/compact decisions (mk:context-engineering).

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Vulnerability analysis: OWASP Top 10, current threat landscape, supply chain security, attack surface mapping, risk prioritization. Use for security audits. NOT for STRIDE/CSO infra audits (mk:cso).

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Runtime router for context decisions: read-more/stop/ask/assume/delegate, minimal read-set, compaction timing. Model: Write/Select/Compress/Isolate. NOT for agent-tree overhead audit (context-audit).

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Systematically QA-tests a web app and fixes bugs: test, then iteratively fix, re-verify, commit each fix. Tiers: Quick, Standard, Exhaustive. Produces before/after health scores and fix evidence.

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Writing tests, running validation, and (TDD mode) red-green-refactor. Active in Test + Build phases. NOT for coverage-gap mapping (mk:nyquist) or sprint contracts (mk:sprint-contract).

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Session-persistent browser automation via Playwright CLI: form filling, screenshots, data extraction, multi-step flows. NOT for autonomous flows (mk:agent-browser) or .spec.ts E2E code (mk:qa-manual).

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Spec-driven manual QA and Playwright E2E generation: navigates apps like a human tester, producing reports or .spec.ts files. Prompts for credentials. NOT for autonomous flows (mk:agent-browser).

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Reviews a GitHub PR with a shallow correctness/security/breaking/AI-slop checklist and emits a verdict; optionally posts via gh. NOT for own-diff audit (mk:review); NOT for replying (mk:respond-pr).

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YC Office Hours-style validation for a new idea before code exists: tests demand (Startup mode) or develops an unvalidated idea (Builder mode). For reviewing an existing plan use mk:plan-ceo-review.

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Maps test coverage to plan acceptance criteria and flags requirements with no tests. Use during Test/Review phases. NOT for running tests (mk:testing); NOT for structural review (mk:review).

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