“driven”的搜索结果

Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.

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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.

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Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversion, --dehydrated for cloud workflows, and when Datasets is/isn't the right tool.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

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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, SES), 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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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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Audit whether a "current product focus receipt" (Decision/Now/Why-now/Evidence/Not-now/Cut-suspend/First-visible-proof/ Acceptance-gate/Kill-revisit-trigger/Owner/Review-date) and the work order it gates state a real, testable decision and a real agent launch — not planning-placeholder prose that sounds like an assignment but can't be proven. Use when deciding whether to launch an agent chain against a milestone or a stated "focus," when a work order lacks explicit input/output/owner/proof-gate, or when an acceptance gate would only prove a cached UI state instead of daemon truth. NOT for distinguishing roadmap items from energy-driven sidequests (legible-roadmap-with-sidequests), reviewing a PRD/prototype for product-completeness gaps like cold start or pricing (product-reality-reviewer), or accepting already-finished work against a personal acceptance bar (port-daddy-user-surrogate-pm-review).

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CQRS pattern, event stores, projections, eventual consistency. Activate on: CQRS, event sourcing, event store, read model, projection, aggregate, domain event, command handler. NOT for: message broker setup (use event-driven-architecture-expert), database optimization (use data-warehouse-optimizer).

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Choose, compare, and decompose work into the right coordination topology: dag, workflow, manager-driven team, swarm, blackboard, team-builder, or recurring loop. Use when the coordination shape is unclear, when you need topology-native breakdown instructions instead of a generic DAG, or when planning topology and runtime topology may differ. NOT for actual execution, node-level skill matching, or framework/tool installation.

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Use for insight, reframing, contradiction, impasse, and anomaly-driven problem solving when execution effort no longer helps. NOT for routine optimization, error correction, or well-specified tasks with known solution paths.

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Expert-level idiomatic Rust API design — the patterns that make illegal states unrepresentable and abstractions zero-cost. Type-state programming (PhantomData state machines), newtype + sealed + extension traits, typestate builders, RAII guards & Drop ordering, the interior-mutability decision tree (Cell/RefCell/Mutex/RwLock/Atomic/OnceLock), enum-driven state machines, error architecture (thiserror vs anyhow), dyn vs generic dispatch & object safety, the impl Trait / GAT / RPITIT toolbox, and Deref-for-smart-pointers (and its abuse). Use when designing a Rust library's public API, encoding invariants in the type system, choosing a dispatch or error strategy, or reviewing Rust for idiom. NOT for borrow-checker firefighting / toolchain / test-runner workflow (use rust-development-workflow), NOT for pd-console GPUI rendering/layout/panes (use gpui-rust-console), NOT for app packaging/notarization (use rust-app-distribution).

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Programmatic SEO planning and analysis for pages generated at scale from data sources. Covers template engines, URL patterns, internal linking automation, thin content safeguards, and index bloat prevention. Use when user says "programmatic SEO", "pages at scale", "dynamic pages", "template pages", "generated pages", or "data-driven SEO".

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This skill should be used when the user wants to "investigate a bug", "debug an issue", "figure out why something is happening", "find the root cause", "troubleshoot", "強い推論で調査", "仮説を立てて検証", "原因を特定", "バグの原因調査", "なぜ動かないか調べて", "問題を切り分け", "原因不明", "デバッグ", or mentions systematic hypothesis-driven debugging. NOTE: Use this for investigating UNKNOWN causes, not for validating design proposals (use devils-advocate for that).

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Save durable preferences, decisions, project facts, commitments, and lessons cheaply with knowledge_remember, or short notes and page updates with attribution and readback. Use for explicit saves or agent-driven remembering when Knowledge is the selected memory provider.

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Elite UX/UI & Advanced GSAP Motion Engineer. Enforces Python-driven true randomization for layout variance, strict AIDA page structure, wide editorial typography (bans 6-line wraps), gapless bento grids, strict GSAP ScrollTriggers (pinning, stacking, scrubbing), inline micro-images, and massive section spacing.

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Pushes interfaces past conventional limits with technically ambitious implementations — shaders, spring physics, scroll-driven reveals, 60fps animations. Use when the user wants to wow, impress, go all-out, or make something that feels extraordinary.

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Write acceptance tests before unit tests to ensure you're building the right thing

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DDD architecture knowledge base. Provides patterns, antipatterns, and PHP-specific guidelines for Domain-Driven Design audits.

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Law-driven abstraction protocol: evidence first, seam test, minimal algebra, executable law check.

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Run TDD cycle for feature implementation. Use when implementing features with RED-GREEN-REFACTOR, running test-driven development, automating TDD workflow, or ensuring test-first development.

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Generate A2UI 0.8 protocol compliant UI code. Use when building agent-driven interfaces, generating JSONL messages for surfaceUpdate/dataModelUpdate/beginRendering, creating forms, lists, cards, or any UI components that render across web/mobile/desktop platforms.

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RFC-driven multi-agent DAG execution pattern with quality gates, merge queues, and work unit orchestration.

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