「rop」の検索結果

Enforce architectural rules when generating or modifying code, and validate proposed designs before approval (design mode). Defaults to clean architecture; supports any architecture style via the architecture-refiner. Validates layer responsibilities, dependency direction, and structural constraints using the loaded architecture rules. Use when generating code, reviewing architecture, creating new files, or when the user mentions 'architecture', 'layers', 'structure', 'dependency rules', 'hexagonal architecture', 'ports and adapters', 'modular monolith', or 'onion architecture'. Also use when reviewing generated code for structural compliance.

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Apply DDD tactical patterns when working with domain code, and validate proposed domain models before approval (design mode). Enforces aggregate design, value objects over primitives, entity identity rules, and bounded context boundaries. Use when creating or modifying domain models, designing aggregates, working in the domain layer, or when the user mentions 'domain', 'aggregate', 'value object', 'entity', 'bounded context', or 'DDD'.

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Grounded in first principles, rigorously examine and refine a user's plan, task, decision, goal, strategy, proposal, or idea through structured, progressively deeper questioning, in order to bridge the gap between the User and the Agent. Use when the user explicitly requests grilling, challenge, pressure-testing, cross-examination, red-team review, pre-mortem analysis, or a decision audit. The goal is to uncover unclear objectives, hidden assumptions, contradictions, weak evidence, missing information, overlooked constraints, dependencies, risks, trade-offs, failure modes, and misalignment between intended outcomes and likely real-world results. Begin by establishing a shared understanding of the user's actual intent, goals, constraints, and success criteria. Ask focused, high-leverage questions rather than broad or repetitive ones. Adapt each question based on previous answers, probing deeper where uncertainty, unsupported assumptions, or strategic weaknesses remain. Regularly summarize the current understanding of the user's intent and position to confirm alignment, expose misunderstandings, and refine the problem or goal definition. Distinguish facts, assumptions, hypotheses, and unknowns. Challenge reasoning rigorously while remaining constructive, respectful, and solution-oriented. Continue until the reasoning is internally coherent, evidence-aware, constraint-conscious, risk-assessed, and translated into a clearer, more actionable goal, decision, or plan. Ultimately, achieving the super-alignment.

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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector graphics for presentations, or ensuring consistent figure styling across analyses.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, choosing the correct hit-calling method by experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.

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Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.

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Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.

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Build circular genome visualizations using circlize (R), pyCirclize (Python), or Circos (Perl CLI) with ideogram tracks, multi-data tracks (scatter, histogram, heatmap), chord/link arcs for interactions, and explicit circos.clear() between plots. Covers when circular is appropriate vs when Cartesian wins (Cleveland-McGill 1984), karyograms, and chromosome adjacency in chord diagrams. Use when adjacency on the circle conveys meaning — chromosome-level overview, structural variants, Hi-C interactions, cross-genome comparisons.

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Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival models from clinical and omics features. Use when predicting patient survival or modeling time-to-event outcomes.

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Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation. For standard design, use proteinmpnn. For ligand-aware design, use ligandmpnn.

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。

Workflow for fine-mapping, colocalization, mediation, pleiotropy analysis, and Mendelian randomization.

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。

Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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When the user wants to create sales collateral, pitch decks, one-pagers, objection handling docs, or demo scripts. Also use when the user mentions 'sales deck,' 'pitch deck,' 'one-pager,' 'leave-behind,' 'objection handling,' 'deal-specific ROI analysis,' 'demo script,' 'talk track,' 'sales playbook,' 'proposal template,' 'buyer persona card,' 'help my sales team,' 'sales materials,' or 'what should I give my sales reps.' Use this for any document or asset that helps a sales team close deals. For competitor comparison pages and battle cards, use an available competitor-analysis capability. For marketing website copy, cold outreach, or offer design, use the corresponding capability when available.

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Internal — for Boundless team members only. Cross-reference Boundless indexer API data, broker telemetry, and service logs to investigate production and staging operational issues. Use when the user wants to understand why slashings happened on prod/staging, diagnose prover or service failures in deployed environments, correlate market events with broker behavior, investigate fulfillment rate drops, look at prover/service logs, or perform any analysis that requires combining on-chain indexer data with off-chain broker telemetry and CloudWatch logs. Also use when the user asks to "investigate", "diagnose", or "find root cause" for prover, service, or market issues on live networks. Do NOT use for debugging local code changes, reviewing PRs, or investigating issues in the codebase itself.

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Structured persuasion for tech leads, PMs, and founders—not activity logs. Five scenarios (kickoff, status update, wrap-up, investor pitch, solution selling) on one 5-part framework (Hook→Context→Proposal→Evidence→Ask). AI prompts for missing materials and audience context; pre-submit checklist. Claude Code plugin; Cursor, Codex, and chat via prompts.

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Block a sender so their messages are dropped before decryption (and the relay is told to refuse their resends); re-allow one with `--remove`, or list blocked senders with `--list`. Use to stop unwanted or abusive mail from a specific sender, undo a block, or audit your block list. If the sender is not specified, ask with AskUserQuestion.

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CustomShader authoring — vertexShaderText and fragmentShaderText against VertexInput, FragmentInput, FeatureIds, Metadata, czm_modelMaterial. Use when reading EXT_mesh_features or EXT_structural_metadata property textures/tables, vertex displacement, or shading VoxelPrimitive.

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。