「boundary」の検索結果

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-stage (pileup + full-alignment) deep-learning caller, selecting the chemistry- and basecaller-version-matched model, enabling read-based phasing, and benchmarking against GIAB with stratification. Covers why the model string is the experiment (no auto-detection, silent degradation on mismatch), why ONT homopolymer/STR indels are the residual error whole-genome F1 hides, and the somatic/trio/RNA boundary to the ClairS/Clair3-Trio family. Use when calling germline SNVs/indels from ONT or HiFi BAMs, choosing a Clair3 model, phasing variants, or benchmarking long-read calls.

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Phases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) with WhatsHap, LongPhase, or HiPhase, and haplotags the BAM (HP/PS tags) for allele-resolved downstream analysis. Covers why phase blocks break at het-sparse gaps (read length x heterozygosity), why phasing the VCF is useless until the BAM is haplotagged, the GT-pipe/PS and read HP/PS tag spec, reporting block N50 with switch error, the diploid-assumption/CNV/haploid-region traps, trio phasing as the gold standard, and the boundary to statistical panel phasing. Use when phasing long-read variants, haplotagging reads for allele-specific methylation/expression or phased SVs, choosing WhatsHap vs LongPhase vs HiPhase, trio phasing, or assessing phasing quality.

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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity data-driven thresholds, flowClust model-based gates), organized as a hierarchical GatingSet (flowWorkspace) and round-tripped with FlowJo via CytoML. Covers the canonical gate order (time -> debris -> singlets -> live -> lineage), FMO-vs-isotype boundary setting, gate-order dependence and recompute semantics, rare-event/MRD gating, and per-population statistics. Use when building a gating strategy, automating a manual FlowJo scheme across samples, choosing manual vs data-driven gates, or extracting population frequencies.

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Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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End-to-end finite element analysis in MATLAB PDE Toolbox — geometry creation, model setup, solve, and post-processing in one skill. Use when building geometry from primitives or file import, setting up femodel with BCs/loads/materials, solving thermal/structural/EM problems, and extracting or visualizing results. Covers fegeometry, multicuboid, multicylinder, multisphere, decsg, boolean ops, mesh generation, femodel, all AnalysisTypes (thermalSteady, thermalTransient, structuralStatic, structuralTransient, structuralModal, structuralFrequency, electrostatic, magnetostatic, dcConduction, harmonic EM), materialProperties, faceBC, faceLoad, cellLoad, vertexLoad, solve, interpolation, von Mises stress, principal stress, reaction forces, heat flux, pdeplot3D visualization. Triggers on: PDE Toolbox, finite element, FEA, thermal analysis, structural analysis, electromagnetic analysis, femodel, mesh, boundary conditions, stress, displacement, heat transfer, post-processing.

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Experimental Vulkan AST-to-LLVM-to-SPIR-V backend, its fail-closed runtime-interface boundary, LLVM build integration, and validation path.

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Public entry point for native device capabilities and native controls — camera, image picker, barcode/QR scanner, document picker, file picker, secure storage, file system, sharing, haptic feedback, PDF generation/viewing, pen/signature capture, background GPS/geolocation tracking, or supported local file workflows — in a Power Apps mobile app. Also owns routing to internal camera/PDF/pen/geolocation implementation helpers and the guidance boundary between native wrappers and Dataverse File/Image host controls.

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Evaluate architecture and module boundaries for volatility-based decomposition using Juval Lowy's framework (from "Righting Software", building on Parnas 1972). Use when reviewing module splits, service boundaries, new abstractions, or any decomposition decision. Trigger on phrases like "where should this boundary be", "how to split this", "module boundaries", "encapsulate change", "volatility", or references to Lowy, Parnas, or "Righting Software". Complements /hickey (interleaved concerns) with a different lens (change encapsulation).

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Expert guidance for FedRAMP certification and compliance under CR26 (FedRAMP Consolidated Rules for 2026). Use this skill whenever a user asks about FedRAMP authorization, ATO (Authority to Operate), cloud security for federal government, NIST SP 800-53 controls, CSP compliance, or any of the core FedRAMP document types: SSP, SAP, SAR, POA&M, CIS/CRM workbooks. Also trigger for questions about FedRAMP Certification Classes (A, B, C, D — new baseline labels: A = pilot/transitional, B = LI-SaaS/Low, C = Moderate, D = High, per NTC-0004), FedRAMP 20x (now the primary authorization pathway), OSCAL mandate (September 2026), 3PAO assessments, continuous monitoring (ConMon), gap assessments, system boundary definition, or architecture reviews for federal cloud. FedRAMP Ready retired July 28, 2026 (Legacy FedRAMP Ready). When in doubt, use this skill — it covers the full FedRAMP lifecycle from readiness through continuous monitoring.

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Removes freeze boundary. Hooks remain registered but allow everything.

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。

Combines careful + freeze. Dual protection: destructive command warnings plus edit boundary enforcement.

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。

Expert guidance for FedRAMP certification and compliance under CR26 (FedRAMP Consolidated Rules for 2026). Use this skill whenever a user asks about FedRAMP authorization, ATO (Authority to Operate), cloud security for federal government, NIST SP 800-53 controls, CSP compliance, or any of the core FedRAMP document types: SSP, SAP, SAR, POA&M, CIS/CRM workbooks. Also trigger for questions about FedRAMP Certification Classes (A, B, C, D — new baseline labels: A = pilot/transitional, B = LI-SaaS/Low, C = Moderate, D = High, per NTC-0004), FedRAMP 20x (now the primary authorization pathway), OSCAL mandate (September 2026), 3PAO assessments, continuous monitoring (ConMon), gap assessments, system boundary definition, or architecture reviews for federal cloud. FedRAMP Ready retires July 28, 2026. When in doubt, use this skill — it covers the full FedRAMP lifecycle from readiness through continuous monitoring.

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Structure a decision or design challenge through multiple perspectives before committing to action. Use as a synthesis step after scoping, mapping, and dilemma navigation when a group needs a wiser next step.

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Map which elements of an assignment benefit from AI assistance vs. which AI use undermines. Use when redesigning tasks for AI-age classrooms or setting defensible AI use policies for specific assignments.

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On-demand procedures for the ComfyUI sidebar panel agent that are too long to sit in the system prompt. Read it when a task lands in one of these areas. subgraph boundary rails and blueprint reuse, merging or composing workflows across tabs, pinning your edits to one workflow, opening staged or downloaded workflow files, untangling Get/Set-bus and rgthree toggle-heavy graphs, authoring rgthree Fast Groups nodes, the LoRA Manager autocomplete-node limitation, the CivitAI browser flow, downloading model weights, reading hardware and runtime stats, Prompt Director audits, custom-node crash recovery, run-to-node render debugging, and multi-stage pipeline chaining. Each section is a lookup, not background reading. Reach for the one you need instead of guessing, and follow the tool's own description for parameter detail.

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Validate and constrain untrusted input at the boundary. Use on any handler that accepts external data.

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Test the boundary between two systems by the contract, not the implementation. Use for APIs, integrations, and shared interfaces.

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Design mandates for acceptance tests - hexagonal boundary, business language abstraction, user journey completeness, pure function extraction, 3 Pillars (domain language / chained narrative / production composition), and the layered ATD discipline (Universe-bound assertion, layer-dependent PBT mode, two-tier acceptance, example-based sad paths)

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Review dimensions for acceptance test quality - happy path bias, GWT compliance, business language purity, coverage completeness, walking skeleton user-centricity, priority validation, observable behavior assertions, traceability coverage, and walking skeleton boundary proof

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Monthly, file work only, no browser at all. Re-reads a month of real change outcomes and rewrites the file that decides what the fix runner may change without asking first. A class the member merged unchanged repeatedly widens by exactly one step. A class they edited, closed unmerged, or that regressed narrows immediately. It never touches the outer boundary, which no volume of evidence can widen.

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Audits PR diffs for architecture boundary violations, design simplicity, dependency drift, and established-pattern mismatches. Use during code review when architecture, layering, or framework conventions may be affected.

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Test Python services with pytest, async coverage, monkeypatch, and boundary-focused fakes. Use when writing Python tests, fixtures, async tests, regression tests, or dependency-isolated verification.

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。