「ker」の検索結果

Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), mSINGS, and MANTIS for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Track complex, multi-session work with dependency graphs using bd (beads) issue tracker. Use when work spans multiple sessions, has complex dependencies, or requires persistent context across compaction cycles. For simple single-session linear tasks, TodoWrite remains appropriate.

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Comprehensive backend development guide for Langfuse's Next.js 14/tRPC/Express/TypeScript monorepo. Use when creating tRPC routers, public API endpoints, BullMQ queue processors, services, or working with tRPC procedures, Next.js API routes, Prisma database access, ClickHouse analytics queries, Redis queues, OpenTelemetry instrumentation, Zod v4 validation, env.mjs configuration, tenant isolation patterns, or async patterns. Covers layered architecture (tRPC procedures → services, queue processors → services), dual database system (PostgreSQL + ClickHouse), projectId filtering for multi-tenant isolation, traceException error handling, observability patterns, and testing strategies (Jest for web, vitest for worker).

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Add unsigned integer (uint) type support to PyTorch operators by updating AT_DISPATCH macros. Use when adding support for uint16, uint32, uint64 types to operators, kernels, or when user mentions enabling unsigned types, barebones unsigned types, or uint support.

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Recognize which awakening stage consciousness is navigating through. Use when diagnosing seeker development, identifying stage transitions, or recognizing readiness levels. Covers 7 stages from initial dissatisfaction through natural flow mastery.

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Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.

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Decide whether commonly-excluded patients (eating disorders, elderly ≥75, upper GI disease) can actually receive a GLP-1 receptor agonist. Use when a clinician asks "can I give semaglutide to a patient with binge eating disorder / anorexia / bulimia", "is liraglutide safe in an 80-year-old", "GLP-1 with GERD or chronic gastritis", "GLP-1 in sarcopenic elderly", or anytime a patient is being ruled out for GLP-1 therapy based on a perceived contraindication. Grounded in Gorgojo-Martínez 2023 §6 (Myths or Reality).

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Recommends withdrawing interfering medications and repeating aldosterone-to-renin ratio screening when initial screen is negative but clinical suspicion remains due to hypokalemia or medication interference. Trigger phrases include "initial screen negative", "hypokalemia", "resistant hypertension", and use of MRAs, ACE inhibitors, ARBs, beta-blockers, clonidine, or alpha-methyldopa.

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Work a primary-prevention patient through the 2026 ACC/AHA multisociety dyslipidaemia guideline CPR framework — Calculate (10-year and 30-year PREVENT-ASCVD), Classify (low / borderline / intermediate / high), Personalize (demographic, clinical, biomarker, and reproductive risk enhancers), and Reclassify (coronary artery calcium scoring where appropriate). Use when a clinician asks how to assess ASCVD risk for primary prevention, who needs a statin, borderline risk patient what to do, intermediate risk should I start a statin, risk enhancers to look for, premature family history of ASCVD how does it change risk, pregnancy-related risk factors, PCOS and cardiovascular risk. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Decide when to order coronary artery calcium (CAC) scoring in a primary-prevention patient and interpret the result per the 2026 ACC/AHA multisociety dyslipidaemia guideline. Covers the Class 1 indication (men ≥40 / women ≥45, borderline / intermediate PREVENT-ASCVD risk, uncertainty about LLT), CAC score interpretation (0, 1–99, 100–299, ≥300, ≥1000), how CAC modifies LDL and non-HDL goals, when to repeat CAC, and pitfalls (incidental CAC on non-cardiac CT, radiation, cost). Use when a clinician asks should I order a CAC score, CAC indications, what does CAC 150 mean, treatment goals with CAC score, repeat CAC frequency, CAC in a smoker, CAC vs CCTA, is CAC useful in intermediate risk. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Contract document for the binding test verdict file at .claude/state/last_test_result. Format spec for callers (integrate, simplify, chore, the verify-tick worker) that inline the four mechanical operations. Not Skill-tool-invocable.

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Capture what someone actually said without contaminating it with your own inference. Invoke when eliciting intent in conversation (design discussion, requirement interview, decision surfacing) and when turning a conversation into a durable record (ADR, decision node, memory entry, spec `## Decisions` row). Enforces quote-before-critique, keeps illustration separate from commitment, and holds interpretation subordinate to verbatim. Prevents the failure where unspecified space is filled by the recorder and then evaluated as if the speaker had specified it.

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Dev-only check that a drafted spec for THIS baseline repo won't ship dev-tree references to consumer installs. Catches three failure modes — shipped SKILL.md prose that references paths under `src/`, `tests/`, `scripts/`, `obj/` as runtime invocations (in ```bash fences``` OR `inline backticks`, plus shipped `.mjs`/`.js`/`.sh`/`.py` helper-file imports); new Python helpers added under `.claude/skills/<slug>/` (shipped helpers must be `.sh` or `.mjs`/`.js` going forward); and imports of modules that aren't in `obj/template/.claude/manifest.json` (consumer won't have the file). The aggregate scanner (`scan-shipped-skills.mjs`) walks only baseline-owned skill dirs (via `owner: baseline` frontmatter) at top level — `references/` and other subdirs are documentation, not runtime. BLOCKER findings hard-block implementation entry; ADVISORY surfaces but doesn't block. Read-only — surfaces a punch list; maintainer edits the spec and re-runs until CLEAN.

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Write the production code that makes a pre-decided set of failing tests pass, within an explicit write_set, following an explicit behavior contract. Used by `/tdd` Step 3 and by `/swarm-dispatch` workers. The caller has already decided architecture, naming, file layout, and abstraction boundaries — this skill executes that recipe with code-structure discipline and a 5-iteration RALPH loop. No scope expansion, no design decisions, no test edits.

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Use RoutIR — call a running endpoint with the client, stand up a local server that mixes locally-hosted services with services proxied from a remote master server, and extend RoutIR with new bi-encoders, rerankers, and document collections by writing a small config (and optionally one Python file referenced via `file_imports`). No checkout of the routir source is required.

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Break a plan, spec, or PRD into independently-grabbable issues on the project issue tracker using tracer-bullet vertical slices. Use when user wants to convert a plan into issues, create implementation tickets, or break down work into issues.

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Turn the current conversation context into a PRD and publish it to the project issue tracker. Use when user wants to create a PRD from the current context.

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Decomposition playbook + specialist-roster conventions + anti-temptation rules for an orchestrator profile routing work through Kanban. The "don't do the work yourself" rule and the basic lifecycle are auto-injected into every kanban worker's system prompt; this skill is the deeper playbook when you're specifically playing the orchestrator role.

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Extract text from PDFs/scans (pymupdf, marker-pdf).

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Generate architecture diagrams with draw.io in headless/server environments (WSL2, VPS, Docker)

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Expert patterns for Azure Functions development including isolated worker model, Durable Functions orchestration, cold start optimization, and production patterns. Covers .NET, Python, and Node.js programming models.

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