'structural analysis' 검색 결과

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

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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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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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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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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).

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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.

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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.

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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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Review all changes in a pull request or branch against its base branch. Use a knowledge graph, a map of code relationships, to report affected files and functions, test coverage, API compatibility issues, and recommended actions.

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• Reviewing all commits in a pull request
• Checking a branch's changes against its base
• Finding callers missed by public API changes

Get structured feedback on a legal memo, brief, paper, or exam essay without having it rewritten. Review organization, reasoning, clarity, and citation form, with three prioritized improvements and a record of recurring writing patterns.

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• Reviewing the structure of a legal memo
• Checking how rules connect to facts and counterarguments
• Prioritizing improvements before revising a draft

Plan and implement features with a workflow that adapts to their complexity. It connects testable requirements to tasks, tests, and small commits, then checks the finished work against the specification through an independent verification pass.

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• Define testable requirements for a new feature
• Implement a large feature through small, verified tasks
• Check whether an implementation meets its specification

Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.

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Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.

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A comprehensive auditor for any agent skill — including Manus, OpenClaw/ClawHub, Claude, LobeHub, or custom SKILL.md-based skills. Use this skill whenever a user wants to evaluate, audit, review, score, or quality-check an agent skill before publishing, updating, or deploying. Covers two hard veto gates (structural redlines + research integrity redlines), static quality scoring across 25 criteria (ISO 25010 + OpenSSF + Agent), dynamic test input generation, multi-mode execution testing, multi-layer output evaluation with five specialized category rubrics (Evidence Insight / Protocol Design / Data Analysis / Academic Writing / Other), a Research Veto that applies to all four research categories, human eval viewer generation, actionable P0/P1/P2 optimization recommendations, and automatic skill improvement that outputs a polished, production-ready SKILL.md. Also use whenever a user says "audit my skill", "evaluate my skill", "improve my skill", or wants a corrected version after evaluation.

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Compress tool outputs, logs, and JSON before they enter the context window — structural compression via a deterministic stdlib script (schema + samples + stats instead of 300 raw rows), no API, no summarization loss. Use when asked shrink this tool output, my context is full of JSON, compress these logs before analysis, or stop wasting tokens on raw data. Produces the crushed artifact with its token math shown, the crush-or-keep decision rules, and the fetch-the-original escape hatch.

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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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Record a dated snapshot of the vault's health numbers and compare against previous snapshots so trends are visible. Use this skill for a monthly or quarterly check, when the user asks whether the vault is improving, or asks to track its numbers over time. Do NOT use for a one-off graph analysis, which is second-brain-graph, or for structural repairs.

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Architectural style selection decision matrices, trade-off analysis, structural enforcement rules, and combination patterns. Load when choosing or evaluating architecture styles.

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Assess project-wide structural technical debt: complexity hotspots, deprecated API usage, duplication clusters, architecture rot, and low-value tests. Ranks findings by impact and refactor effort into a report at .turbo/technical-debt.md. Use when the user asks to "assess technical debt", "find technical debt", "review technical debt", "what should we refactor", "find refactoring candidates", "where is the code rot", "what's our worst code", "find low-value tests", or "which tests can we delete". Analysis-only — does not modify code.

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Use code-review-graph for local-first CLI/MCP code knowledge graphs, graph-backed code review, structural search, and repository-analysis integrations.

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Produce a standalone test plan by analyzing code for test coverage gaps and edge cases. Use when you need to create, generate, or draft a test plan for a branch, need to analyze test coverage, or need to identify what tests to write for specific files or directories. Does not produce a plain-language plan for a person to run tests by hand — use manual-test-planning for that. Does not write test code — use tdd to implement behavior test-first. Does not refine existing plans — use iterative-plan-review. Does not review code quality, security, or style — use code-review for full code review. Does not evaluate architectural testability or structural coupling — use architectural-analysis for architectural assessment.

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Produces a human-readable, progressive-disclosure overview of unfamiliar code or a pull request's changes — why it exists (the real problem it solves or goal it serves for the business or a user), and from there what it does, how it flows, and where to start — so you can get up to speed before working on or reviewing it. Use when you want to understand, get oriented in, make sense of, explain, or get up to speed on a chunk of code, a file, a directory, a symbol, or a PR's changes. Writes the overview to a scratch file and changes no code. Does not review code quality or raise findings — use code-review for auditing changes or post-code-review-to-pr for posting them. Does not produce durable feature or system documentation — use project-documentation. Does not assess architecture or structural risk — use architectural-analysis. Does not diagnose bugs or root-cause failures — use investigate. Does not pace a person through the code one step at a time in conversation — use code-walkthrough.

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