「coverage」の検索結果

Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.

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。

Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

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 somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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。

Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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。

Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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 differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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。

Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/MntJULiP/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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。

Find out why the tests pass but the app is broken. Catches false greens: a green suite over a feature that does not work, a mocked API standing in for a real one, an assertion that holds no matter what the app does, a click handler wired to nothing. Use when the suite is green and the user says it is broken, when a test never fails, when coverage looks fine but bugs still ship, or before trusting a passing run you did not watch.

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。

Turn a user journey you just clicked through into a saved regression check that re-runs deterministically, with no model in the loop and no test code to write. Use when you have driven the same flow twice, when the user wants regression coverage without a Playwright suite, when a refactor needs proving against every existing journey, or when re-verifying by hand is costing a full drive every time.

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。

Writes turn-level tests for a LiveKit agent in the user's normal test suite: pytest (Python) or Vitest (Node.js). Use when the user asks to "write tests for my agent", "add a test for this tool", "test the handoff", "pin this bug", "why does my agent test fail", or after building or changing agent behavior that needs regression coverage. Covers the SDK's test session harness, assertions on messages, tool calls and handoffs, LLM judging of a reply against an intent, mocking tools, multi-turn tests, and judging whole conversations with the built-in judges. For interactive poking use debugging-livekit-agents. For grading whole conversations at scale use running-livekit-simulations.

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。

Generate and structure MATLAB unit tests using matlab.unittest and matlab.uitest features, including class-based tests, parameterized testing, fixtures, mocking, and app testing with gestures. Use when writing, generating, or adding tests, creating test classes, adding test methods, parameterizing tests, setting up fixtures, mocking dependencies, or testing App Designer apps. Do NOT use for running tests, collecting coverage, or CI/CD configuration.

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。

Generate driving scenes, scenarios, road surfaces, and 3D content from scenariobuilder.* sensor data (GPS, camera, lidar, actor tracks) using Scenario Builder for Automated Driving Toolbox. BUILD, EXPORT, or AUGMENT a virtual scenario/scene/map: ego or actor trajectories, trajectory smoothing, OpenCRG road-surface extraction, 3D asset generation, static-object placement, point-cloud georeferencing + elevation, lane-based ego localization, sensor-fusion tracking, scenario-event extraction (cut-ins, hard brakes, near-misses, ADAS disengagements), or export to RoadRunner, drivingScenario, OpenDRIVE, OpenCRG, OpenSCENARIO, or Unreal Engine. Also: log-to-scenario, scenario harvesting, accident/near-miss reconstruction, SOTIF (ISO 21448) and ISO 26262 scenario coverage, USGS-aerial-lidar augmentation, traffic-sign placement, vision-based vehicle classification for actor assets. NOT for raw-data import or multi-sensor sync/crop/offset/timestamp normalization — route those to matlab-import-driving-data.

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。

Use when creating a test plan for a blast radius. Assigns all 4 tiers (fully-automated, hybrid, agent-probe, known-gap) with exact commands, what each proves, and gap resolution options.

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。

Run release-readiness checks for this repository. Use when validating docs, scripts, verification coverage, and operational safety before merge or release.

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。

All-in-one project configuration and health management. Sets up new projects (settings.local.json, CLAUDE.md, .gitignore), audits existing projects (permissions, context quality, MCP coverage, leaked secrets, stale docs), tidies accumulated cruft, captures session learnings, and adds permission presets. Uses sub-agents for heavy analysis to keep main context clean. Trigger with 'project health', 'check project', 'setup project', 'kickoff', 'bootstrap', 'tidy permissions', 'clean settings', 'capture learnings', 'audit context', 'add python permissions', or 'init project'.

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。

Set up Vitest testing in any project — detects type (Cloudflare Workers, React, Node, library), generates vitest.config.ts, test setup, utilities, and a sample test. Covers mocking patterns, coverage config, workspace setup, Jest migration. Use whenever the user mentions adding tests, setting up Vitest, configuring tests, migrating from Jest, fixing testing infrastructure, or asks 'how do I test this'.

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。

Map contest attachments to subquestions, audit and clean raw data, and emit one reusable data profile with quality, coverage, imbalance, concentration, and method-readiness evidence for downstream risk screening.

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。

Plan, audit, implement, migrate, or validate localization for multilingual products and websites, including locale scope, market readiness, URL architecture, content coverage, hreflang coordination, rollout, and production verification. Use translation for the actual translation, glossary, and language review work.

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。

When the user wants to fix indexing issues from Search Console, use noindex, or implement Google Indexing API. Also use when the user mentions "fix indexing," "not indexed," "Crawled - currently not indexed," "discovered - currently not indexed," "index coverage," "noindex," "noindex tag," "pages not indexed," "why not indexed," "request indexing," or "Google Indexing API." For sitemap, use xml-sitemap.

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。

When the user wants to analyze Google Search Console data, use the GSC API, or interpret search performance. Also use when the user mentions "GSC," "Search Console," "indexing report," "Core Web Vitals," "Enhancements," "Insights report," "search performance," "search queries," "search performance report," "URL inspection," "impressions," "CTR," "average position," "index coverage," "GSC data analysis," "Search Console API," or "searchanalytics.query." When the user wants to rewrite title tags (not only report on them), use title-tag. For meta description rewrites, use meta-description.

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。

Iterative measurement-driven improvement loop. Measure, profile, mutate, re-measure, commit. Works for performance, bundle size, complexity, test coverage — anything quantifiable. Use when the user wants to systematically improve a metric through repeated cycles of profiling and targeted changes.

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。

Audit content gaps and decay using Ahrefs MCP data: missing topics, thin coverage, outdated content, and decaying pages. Use this skill when planning a content roadmap, refreshing a stale catalog, building topical authority, or identifying which existing pages need update versus replacement. Triggers on content gap, content audit, content refresh, content roadmap, decaying content, content decay, topical authority, what topics should we cover, where is competitor content stronger. Also triggers when organic traffic is flat despite consistent publishing.

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。

Plan and execute off-page SEO including link building, digital PR, brand mentions, citation building, and external authority signals. Use this skill whenever the user wants to build backlinks, plan a digital PR campaign, list local citations, run guest post outreach, develop linkable assets, recover lost links, or audit a backlink profile for risk. Triggers on link building, backlinks, digital PR, brand mentions, citation building, guest post, outreach, linkable asset, broken link building, HARO, podcast outreach, off-page SEO, anchor text, link velocity, toxic backlinks, disavow. Also triggers when the user is trying to grow domain authority or earn coverage.

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。

How to author a content brief that actually guides a writer (human or AI) to produce a piece that ranks, converts, or both. Per-piece editorial brief: target keyword and cluster, search intent, audience and JTBD, heading structure, entity coverage for AEO/GEO, internal linking strategy, success criteria. The middle path between thin briefs (a keyword and a deadline) and thick briefs (a 4-page document nobody reads). Triggers on content brief, brief the writer, brief the article, brief authoring, content brief template, brief audit, per-piece brief, editorial brief, target keyword brief, search intent brief. Also triggers when briefing a human writer or an AI agent on a single content piece.

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。