「fact」の検索結果

Use when a plan directory (plan.md + phase-*.md) needs a visual review. By DEFAULT this drives the STRUCTURED visual-plan artifact (visual-plan/plan.json) via the mewkit visual-plan CLI — generate if absent, validate, open the local studio (view/edit), and export plan.html from the approved artifact. Pass --static for the legacy prompt-only single-file plan.html template render. Triggers on "render this plan", "visualize the plan", "open the plan studio", "make a shareable plan page", "plan.html". This is the canonical owner of plan-as-visual-review. NOT for plan critique or scope review (see mk:plan-ceo-review / mk:validate-plan), NOT for generic code/diagram/diff visuals (see mk:preview), NOT for live media generation (see mk:multimodal).

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Use when surfacing architectural friction and proposing deepening refactors (shallow modules → deep modules) for testability and AI-navigability. Triggers on "improve architecture", "find deepening opportunities", "where is this codebase shallow", "architecture review". Emits structured candidates + precise patches; delegates ALL rendering to mk:preview. NOT for diagram/HTML rendering (see mk:preview); NOT for trade-off deliberation (see mk:party); NOT for plan critique (see mk:plan-ceo-review).

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Use when answering factual or explanatory questions about the current project — codebase, architecture, conventions, workflows, constraints — with minimal cited evidence. Triggers on "how does X work here", "what does X mean", "why is X structured this way", "is this claim true in the repo", "explain X with sources". NOT for brainstorming or comparing approaches (mk:brainstorming), trade-off decisions (mk:party), debugging/root cause (mk:investigate), code review (mk:review), plans (mk:plan-creator), security audits (mk:cso), visual explanations/diagrams (mk:preview --explain), test-coverage gaps (mk:nyquist), library docs (mk:docs-finder), or workflow navigation (mk:help).

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Refactor code for better structure and patterns

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Prepare qualified Fusion CAM setups, operations, toolpaths and quarantined NC candidates using explicit manufacturing assets and authority. Never controls physical equipment.

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Take a chosen visual to finished, production-ready state. Runs cleanup + refinement passes (fix artifacts, balance composition, color-grade, sharpen text, conform to spec/aspect) using image edit/regenerate. Use when the user says "polish this", "finalize", "clean up the image", "production-ready", "fix the artifacts", or has a selected visual that needs finishing. Final stage of the Creative Production set.

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Use when user says "simmer this", "refine this", "hone this", "iterate on this", or asks to improve a specific artifact over multiple rounds. Runs an iterative refinement loop with investigation-first judges that read the code, understand the problem, and propose evidence-based improvements. Auto-selects single judge or multi-judge board based on complexity. Works on any artifact type: documents, prompts, specs, emails, creative writing, API designs, pipelines, codebases. Supports multi-file workspace targets, runnable evaluators, and open-ended optimization (model selection, pipeline topology, prompt tuning).

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Test-driven development with red-green-refactor loop. Use when user wants to build features or fix bugs using TDD, mentions "red-green-refactor", wants integration tests, or asks for test-first development.

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Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-stabilizing transforms (logicle/biexponential, arcsinh, log) for flow and mass cytometry. Covers spillover-matrix estimation from single-stain controls, AutoSpill, the spillover spreading matrix and why panel design (not compensation) bounds resolution, compensate-then-transform ordering, and arcsinh cofactor choice (5 for CyTOF, ~150 for fluorescence, per-channel via flowVS). Use when correcting spectral overlap, preparing data for gating/clustering, choosing logicle vs arcsinh, deciding a cofactor, or distinguishing compensation from spectral unmixing.

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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "beat the baseline on this benchmark", "run a search over approaches and keep the best", "do an MLE-bench / Kaggle-style optimization", or any long-horizon "make this artifact better and don't just memorize the dev set" task. Trigger it even when the user doesn't say "Arbor" or "hypothesis tree" but describes repeated experiment-and-evaluate loops, branching exploration of competing ideas, or worries about a dev/test gap. Runs Claude itself as the coordinator with subagent executors in isolated git worktrees; for the standalone `arbor` CLI tool see references/arbor-upstream.md.

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Determines whether bone mineral density (BMD) measurement is indicated when patients have osteoporosis risk factors or have discontinued sex hormone therapy following gonadectomy. Clinical triggers include documented osteoporosis risk factors (e.g., low body weight, glucocorticoid use, prior fracture) or cessation of sex hormone therapy after surgical gonadectomy.

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Evaluates cardiovascular risk factors in persons receiving hormone therapy by obtaining fasting lipid profiles and diabetes screening. Triggered when a patient is on gender-affirming hormone therapy and due for routine cardiovascular risk assessment.

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This skill guides clinicians to assess bolus calculator settings when reviewing pump settings or verifying carb ratio and sensitivity factor during clinic visits. It evaluates insulin-to-carbohydrate ratio, insulin sensitivity factor, glucose targets, and active insulin time for embedded bolus calculators in CSII.

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Evaluates patient-specific factors such as lifestyle, motivation, and barriers that may affect successful CGM use. Triggered when clinicians discuss patient’s readiness for CGM or identify obstacles to consistent sensor wear.

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Use for Six Thinking Hats or de Bono's parallel thinking, or when a decision or idea needs facts, gut feel, risks, benefits and new options kept apart: "look at this from all sides", "full perspective check". Skip for plain factual questions or single-angle hot takes.

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Test-driven development with red-green-refactor loop. Use when user wants to build features or fix bugs using TDD, mentions "red-green-refactor", wants integration tests, or asks for test-first development.

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Generate conservative, editable English outreach drafts for foreign-trade sales from structured lead inputs and customer-intel signals. Use when an operator needs a first-touch or follow-up email draft that calls confirmed recent/customer-market signals from the customer-intel Skill, with subject options, review notes, and explicit reminders not to present unconfirmed facts as facts.

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Builds the "Report Sources" child page for a finished Weekly Community Signal report — an evidence-backed defense of WHY every item landed in the column/section/rank it did. The agent argues each placement like a lawyer (claim → evidence → rule → rebuttal) but is under oath: it CANNOT invent, spin, or overstate — every claim ties to a verifiable fact (issue #, label, PR type, quoted comment, npm output, the front-door test). Not CYA — it's so Nathan can defend the report with facts and see the exact reasoning behind each call. Runs after the report (invoked by weekly-report, last steps) and on "report sources", "defend the report", "why is this here".

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TDD Refactor Phase - Improve code while keeping tests green using Simple Design Rules and APP mass

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Expert-level composites engineering covering fiber reinforced polymers, matrix materials, laminate theory, manufacturing processes, failure modes, and composite design.

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