「structural analysis」の検索結果

Builds and queries multi-language source and binary code graphs for security analysis. Includes pre-analysis passes for blast radius, taint propagation, privilege boundaries, entry point enumeration, proxy/unresolved-call tracking, type/reference queries, structural traversal, graph diffs, audit augmentation, declared cross-language/FFI/external links via `.trailmark/links.toml`, and SQL schema graphs. Use when analyzing call paths, mapping attack surface, finding complexity hotspots, enumerating entry points, tracing taint propagation, measuring blast radius, importing SARIF/weAudit/binary findings, linking source graphs across language or RPC boundaries, or building a code graph for audit prioritization. Feature-gate version-specific Trailmark APIs before using them; prefer `trailmark.parse.detect_languages()` or `--language auto` when the target language is unknown or polyglot.

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Detects duplicate boilerplate, copy-paste tests, and structural maintainability issues across .NET test suites. Use when the user asks to reduce repetition, consolidate similar test methods, convert copy-paste tests to data-driven parameterized tests, suggest a better test structure, or identify refactoring opportunities. Identifies repeated construction, assertion patterns, copy-paste methods convertible to DataRow/Theory/TestCase, redundant setup/teardown, and shared infrastructure. Produces an analysis report with concrete before/after suggestions. Works with MSTest, xUnit, NUnit, and TUnit. DO NOT USE FOR: writing new tests (use writing-mstest-tests), reviewing test quality or anti-patterns (use test-anti-patterns), or deep mock auditing (use exp-mock-usage-analysis).

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This skill covers game-theoretic methods in structural econometrics and industrial organization. Use when the user is working with strategic interactions, equilibrium analysis, or game-theoretic structural models — including entry games, conduct testing, auction models with strategic bidding, bargaining, or matching markets. Triggers on "Nash equilibrium", "subgame perfect", "best response", "strategic interaction", "entry game", "conduct testing", "auction", "mechanism design", "matching market", "bargaining", "BNE", "Bayesian Nash", "static game", "dynamic game", "repeated game", "multiple equilibria", "equilibrium selection", "discrete game", "oligopoly", "game-theoretic", "player", "payoff", "strategy", "dominant strategy", "Bresnahan-Reiss", "Ciliberto-Tamer", "partial identification", "set identification", or markup test.

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Detect structural macro regime transitions (1-2 year horizon) using cross-asset ratio analysis. Analyze RSP/SPY concentration, yield curve, credit conditions, size factor, equity-bond relationship, and sector rotation to identify regime shifts between Concentration, Broadening, Contraction, Inflationary, and Transitional states. Run when user asks about macro regime, market regime change, structural rotation, or long-term market positioning.

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Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline, SQANTI3, and ONT tools (IsoQuant, FLAIR, Bambu, StringTie2). Covers why a novel isoform is an artifact until proven otherwise (RT template-switching, intra-priming, and 5' degradation manufacture junctions and truncations), the SQANTI3 structural categories and their trust order, the Kinnex skera-split step, orthogonal CAGE/poly-A/short-read-junction validation, and why long-read isoform quantification needs EM. Use when building a full-length isoform catalog, classifying/filtering long-read transcripts, running Iso-Seq or ONT cDNA/dRNA analysis, or judging novel-isoform reliability.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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。

Detects duplicate boilerplate, copy-paste tests, and structural maintainability issues across .NET test suites. Use when the user asks to reduce repetition, consolidate similar test methods, convert copy-paste tests to data-driven parameterized tests, suggest a better test structure, or identify refactoring opportunities. Identifies repeated construction, assertion patterns, copy-paste methods convertible to DataRow/Theory/TestCase, redundant setup/teardown, and shared infrastructure. Produces an analysis report with concrete before/after suggestions. Works with MSTest, xUnit, NUnit, and TUnit. DO NOT USE FOR: writing new tests (use writing-mstest-tests), reviewing test quality or anti-patterns (use test-anti-patterns), or deep mock auditing (use exp-mock-usage-analysis).

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JASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis. For ChIP-seq peak motif discovery use homer-motif-analysis; for regulatory variant scoring use regulomedb-database.

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Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, H-bonds, PCA, and custom distance/angle calculations. Use for post-simulation structural analysis; use OpenMM/GROMACS for running simulations.

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Guide for writing ast-grep rules to perform structural code search and analysis. This skill should be used when users need to search codebases using Abstract Syntax Tree (AST) patterns, find specific code structures, or perform complex code queries that go beyond simple text search, or when a simple grep/glob search is insufficient for structural code pattern matching.

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Diagnosis of why structural materials fail — ductile overload, brittle cleavage, fatigue, creep, stress-corrosion cracking, hydrogen embrittlement, and corrosion. Covers Griffith fracture mechanics, the ductile-to-brittle transition, the S-N and Paris fatigue frameworks, fractographic interpretation, and the J.E. Gordon view that strength, stiffness, and toughness are distinct properties that must be understood together to prevent collapse.

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Builds default probability and recovery rate models with industry data, structural analysis, and loss-given-default estimation. Use when modeling credit losses, estimating recovery values, or analyzing default scenarios.

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Detects seven structural anti-patterns in Claude Projects that cause unpredictable output, ignored instructions, and degraded quality. Diagnoses Monolith, Orphan File, Echo Chamber, Phantom Conversation, Kitchen Sink, Misaligned Hierarchy, and Blurred Layers. Use when user says "what's wrong with my project," "Claude ignores my instructions," "diagnose my project," "why is output inconsistent," "review my project setup." Also trigger on symptom-phrased: "Claude doesn't follow my rules," "my instructions keep getting overridden," "my Project isn't behaving as designed." Use alongside rootnode-project-audit if available for deeper structural analysis. Activate whenever the user describes symptoms of unreliable, inconsistent, or degraded Claude Project output, even if they do not name a specific pattern. Do NOT use when the user's primary request is Memory-layer rebalancing (use rootnode-memory-optimization if available) or scoring a single prompt (use rootnode-prompt-validation if available).

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Navigate the Kabbalistic Tree of Life (Etz Chaim) — explore the ten sephirot, twenty-two paths, four worlds, and three pillars. Covers correspondences, contemplative exercises, and structural analysis. Use when exploring a sephira's attributes and divine names, studying structural relationships between sephirot, learning the four worlds (Atzilut through Assiah), tracing a path's Hebrew letter and tarot attributions, or using the Tree as a symbolic map for understanding a concept or system.

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"Apply Structural Equation Modeling (SEM) to test hypothesized causal structures by combining measurement models (CFA) and structural models (path analysis). Use this skill when the user needs to validate latent constructs, test mediation or moderation paths, assess model fit with CFI/TLI/RMSEA/SRMR, or when they ask 'do these variables form a causal chain', 'how do I test my theoretical model', or 'is my measurement model valid'.".

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Structural and functional brain connectivity — tractography, functional networks, and graph-theoretic analysis.

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Multi-pass structural code review with adversarial analysis, scope-aware dispatch, adversarial persona passes, and forced-finding protocol. Supports input modes: branch diff (default), PR number (#123), commit hash, pending changes (--pending). Use when asked to "review this PR", "code review", "pre-landing review", "check my diff", or "review #123". Proactively suggest when the user is about to merge or land code changes. NOT for behavioral verification against a running build (see mk:evaluate); NOT for post-implementation simplification (see mk:simplify).

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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。

Professional network graph analyst identifying Gladwellian superconnectors, mavens, and influence brokers using betweenness centrality, structural holes theory, and multi-source network reconstruction. Activate on 'superconnectors', 'network analysis', 'who knows who', 'professional network', 'influence mapping', 'betweenness centrality'. NOT for surveillance, discrimination, stalking, privacy violation, or speculation without data.

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Mitigate incidental code complexity when control flow is tangled, nesting is deep, names are hard to parse, or reasoning requires cross-file hops. Use when a review stalls on readability, you need an analysis-first refactor plan before edits, or you want essential-vs-incidental verdicts, ranked simplification steps, a small structural sketch, and a TRACE assessment (analysis-only; no edits).

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。

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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。

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Complete workflow for static structural analysis. Use when analyzing stress, displacement, or reaction forces under constant loads. For strength and stiffness evaluation.

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Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

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。