「sca」の検索結果

Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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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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Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

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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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Fetch external sources (web/arXiv/GitHub) into scanner-gated wiki CANDIDATES, never canonical pages: guarded, capped, scanned. NOT for local knowledge (mk:wiki) or markdown fetch (mk:web-to-markdown).

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Domain-aware complexity routing: scans the task for domain keywords, matches domain-complexity.csv, and returns complexity level, workflow intensity, and execution tier. Extends Phase 0 orchestration.

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Workflow navigator: scans project state (plans, reviews, tests, git) and recommends the next pipeline step. Use for 'what next?' or 'where am I?'. NOT for complexity routing (mk:scale-routing).

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Operational decision frameworks: triage, escalation, case management, billing ops. Use for 'how to handle X cases', 'build triage', 'escalation protocol'.

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Create new skills with proper structure, compliance checks, and registration. Use when asked to create a skill, build a new skill, or scaffold a skill template. Enforces mk: prefix, sub-agents.md structure, and context engineering principles.

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Capture, gate, query, and render long-term project knowledge through the gated `mewkit wiki` subsystem. Use to create a wiki, propose/approve candidates (scanner-gated), hand off a skill's terminal artifact as a scanned candidate, recall context, search the FTS index, or list pages. Agents may only PROPOSE candidates; canonical pages are written only via human approve. NOT for short-lived JSON memory (see mk:memory); NOT for fetching external sources (see mk:wiki-research); NOT for HTML snapshots (see mk:wiki-render).

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Use when analyzing harness trace logs to surface recurring failure patterns and suggest harness improvements. Scatter-gather pattern across last N runs with mandatory HITL gate before any change is applied. Triggers on /mk:trace-analyze, "analyze traces", "find patterns in harness runs", or after a model upgrade flagged dead-weight-audit-needed.

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Runs autonomous multi-hour green-field builds: planner, contract, generator/evaluator loop, scaffolding density per model tier. NOT for scoped tasks (mk:cook); NOT for scaffolding only (mk:bootstrap).

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Workflow navigation assistant. Scans project state (plans, reviews, tests, git) and recommends the next step in the 7-phase pipeline. Use when asked "what should I do next?", "where am I?", "help", or at session start. NOT for domain complexity routing (see mk:scale-routing); NOT for skill discovery (descriptions handle that automatically).

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Use when running an autonomous multi-hour build of a green-field product — orchestrates planner → contract → generator ⇄ evaluator loop with adaptive scaffolding density per model tier. Triggers on /mk:autobuild, "build me a kanban app", "build a retro game maker", "autonomous build", or any green-field product spec. NOT for scoped single-task work (see mk:cook); NOT for initial project scaffolding only (see mk:bootstrap).

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Chief Security Officer mode. Infrastructure-first security audit: secrets archaeology, dependency supply chain, CI/CD pipeline security, LLM/AI security, skill supply chain scanning, plus OWASP Top 10, STRIDE threat modeling, and active verification. Two modes: daily (zero-noise, 8/10 confidence gate) and comprehensive (monthly deep scan, 2/10 bar). Trend tracking across audit runs. Use when: "security audit", "threat model", "pentest review", "OWASP", "CSO review".

日本語の概要は準備中です。原文の説明を表示しています。

Advisory model escalation based on task outcome tracking

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Find UX pains and opportunities fast through competitor scans, pattern research, and web search. Surfaces how others solve the same flow, common failure modes, and conventions users already expect. Use when the user says "research this UX", "how do others do X", "competitor scan", "find UX patterns", "what's the convention for Y", or before ideating a flow. Part of the Product Design set. Uses web search/fetch tools.

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Plan and run safe reverse engineering, decompilation, disassembly, instrumentation, de-obfuscation, and anti-analysis countermeasures for binaries, firmware, mobile apps, WebAssembly, JavaScript bundles, and .NET assemblies. Use for behavior reconstruction, cross-layer Electron tracing, REA, reversing strategy, decompiler selection, binary analysis, malware-style triage, unpacking, deobfuscation, defeating anti-debug or anti-VM checks, Wakaru, Ghidra, IDA, RetDec, radare2, Rizin, Frida, angr, YARA, or command scripts that capture analysis stats.

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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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Create exercise directory structures with sections, problems, solutions, and explainers that pass linting. Use when user wants to scaffold exercises, create exercise stubs, or set up a new course section.

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Practical UI refactoring and visual design review inspired by Refactoring UI by Steve Schoger and Adam Wathan. Use when an AI coding agent needs to improve an existing interface, audit visual polish, redesign a rough UI, review frontend code for hierarchy/spacing/typography/color/depth/image issues, or turn a plain implementation into a cleaner product-quality screen. Do not use for creating UI from scratch, scaffolding a new app, building a new landing page, or designing a new design system unless the user explicitly asks to review or refactor an existing interface.

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Use when writing Delphi / FreePascal / C++Builder code that reads, writes, manipulates, or exports Excel (.xlsx / .xls) files, generates PDF or HTML from Excel, or produces data-driven reports with FlexCel Studio for VCL and FireMonkey (TMS FlexCel). Triggers include Excel/xlsx from Delphi, TXlsFile, TFlexCelReport, TFlexCelPdfExport, TFlexCelHtmlExport, FireMonkey Excel export, Lazarus Excel, and Excel reporting from Pascal.

日本語の概要は準備中です。原文の説明を表示しています。