「score」の検索結果

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.

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Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Li & Hart 2019 Genome Med), a bidirectional Z-score method that identifies synthetic-lethal sensitizing genes and resistance-conferring suppressor genes from vehicle vs drug comparisons. Covers vehicle-anchored design (not Day-0), the bidirectional Z math giving 2-3x sensitivity over MAGeCK / STARS / edgeR / RIGER on drug screens, per-gene sumZ and normZ, synth (sensitizer) vs supp (suppressor) FDR, multi-dose handling, integration with control sgRNAs, and comparison with MAGeCK MLE with dose covariate. Use when running a drug-modifier CRISPR screen, identifying sensitizing or resistance genes for a drug candidate, choosing drugZ vs MAGeCK MLE for chemogenomic analysis, troubleshooting low-effect drug screens where MAGeCK lacks sensitivity, or designing a drug-screen layout (vehicle vs drug arms).

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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).

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ESM2 protein language model for sequence scoring, embeddings, and plausibility checks. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai1-structure-prediction or boltz-structure-prediction. For QC thresholds, use protein-design-qc.

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Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or RFdiffusion outputs, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding success rates, (5) Need better ranking than ipTM or iPAE. For structure prediction, use chai or alphafold. For QC thresholds, use protein-qc.

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ESM2 protein language model for embeddings and sequence scoring. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai or boltz. For QC thresholds, use protein-qc.

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Comprehensive guidelines for Obsidian.md plugin development including ESLint rules from eslint-plugin-obsidianmd v0.4.2, TypeScript best practices, memory management, API usage (requestUrl vs fetch), UI/UX standards, popout window compatibility, community.obsidian.md submission process, and Scorecard optimization. Use when working with Obsidian plugins, main.ts files, manifest.json, Plugin class, MarkdownView, TFile, vault operations, or any Obsidian API development.

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Make kinetic-typography motion reels (MP4) in code: showreels, portfolio or work reels, product promos, intro films, "motion design"-style videos with bold condensed type, HUD micro-type, black/cream/lime palette, three.js generative layers (particle terrain, liquid marble, chrome knot, particle clouds), shape-continuity transitions and a synthesized, beat-locked score. Canvas 2D + WebGL rendered frame by frame in headless Chrome, encoded with ffmpeg. Use when the user asks for a reel, showreel, motion-graphics / kinetic-type video, a "Work Reel" in this style, or to extend/re-cut the Work Reel ’26.

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Launches 5 parallel AI agents to produce a comprehensive property analysis with composite Property Score (0-100), investment grade, and actionable recommendations

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Local Market Analysis — median prices, inventory, days on market, price trends, rental conditions, economic drivers, and market classification with Market Score (0-100)

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Evaluates a property across three investment strategies — Buy & Hold, BRRRR, and Fix & Flip — with feasibility scores, multi-year projections, tax benefits, and break-even analysis

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Finds and analyzes 5-10 comparable recent sales to estimate fair market value, calculate price adjustments, and score the property's value proposition

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60-Second Property Snapshot — quick assessment without subagents for fast property evaluation with signal, key factors, and CTA for full analysis

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Commercial Property Analysis — NOI, cap rate, expense ratio, tenant mix, vacancy, debt coverage, replacement cost, and lease analysis with Commercial Score (0-100)

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Professional PDF Property Report Generator — compiles all PROPERTY-*.md analysis files into a polished, client-ready PDF with score gauges, comparison tables, financial projections, and investment recommendations

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Neighborhood Analysis — schools, crime, walkability, demographics, amenities, growth trajectory, and natural disaster risk with Neighborhood Score (0-100)

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Fix-and-Flip Analysis — purchase price, ARV, rehab budget breakdown, holding costs, selling costs, profit margin, ROI, timeline, and risk assessment with Flip Score (0-100)

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Define, track, and act on QA metrics: test coverage percentage, flakiness rate, defect escape rate, MTTR, test execution time trends, automation ROI, quality gates, and SLAs for test suites. Includes metric formulas, realistic targets by company stage, and the action to take when each metric goes red. Use when: "QA metrics," "test metrics," "quality KPIs," "test health," "flakiness rate," "defect escape rate." Not for: building the dashboard UI (Allure/Grafana) — use qa-dashboard; measuring coverage gaps and mutation score — use coverage-analysis. Related: qa-dashboard, coverage-analysis, ci-cd-integration, release-readiness, quality-postmortem.

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Runtime per-test healing with evidence: multi-attribute selector healing, environment-aware diagnosis, flake classification, quarantine management, and confidence-scored auto-repair. Goes beyond simple locator fallbacks to cover action-level healing, data healing, and observable repair workflows. Use when: "flaky test," "test stability," "self-healing locator," "broken locator recovery," "unreliable test," "quarantine flaky test." Not for: bulk regenerating selectors after a planned UI refactor — use selector-drift-recovery (this skill heals ONE test at runtime; that one rewrites many tests offline). Not for: classifying/clustering CI failures into bug reports — use ai-bug-triage. Related: playwright-automation, selector-drift-recovery, ci-cd-integration, qa-metrics, ai-bug-triage.

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Hoyeon Socratic discussion workflow for Codex. Use when the user invokes "$hoyeon-discuss", "/discuss", asks to think through an idea, challenge assumptions, clarify requirements before planning, run a deep/scored discussion, or says Korean phrases like "같이 생각해보자", "문제 정의", "이거 어떻게 생각해?", "요구사항이 불명확", or "아이디어 구체화".

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