「clo」の検索結果

Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.

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Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

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Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.

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Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and the n=3 visualization stake. Use when generating DE diagnostic plots, choosing VST vs rlog for visualization, troubleshooting suspicious plot patterns (shifted MA cloud, batch-dominated PCA, anti-conservative p-value histogram), or building a standard QC figure panel.

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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.

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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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Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversion, --dehydrated for cloud workflows, and when Datasets is/isn't the right tool.

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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, mixed), Hochberg/Hommel/Holm with PRDS, and the closed-testing principle (Marcus-Peritz-Gabriel; Goeman 2021 admissibility). Covers FDA Multiple Endpoints Final Guidance (October 2022), graphical procedures via R gMCP, primary + key-secondary + subgroup hierarchies, and FWER vs FDR distinction. Use when designing the multiplicity strategy for confirmatory trials with multiple primary or key secondary endpoints.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda scheduling, soft-core potentials, MBAR/BAR analysis, cycle-closure validation, and protocol-appropriate enhanced sampling. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Use when building ANY watchOS app — app structure, independent apps, Watch Connectivity, Smart Stack widgets, complications, controls, RelevanceKit, background tasks, ClockKit migration.

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Use when asking about Axiom skills or axbuild build/test capture, xclog console, xcsym .ips/MetricKit/.crash symbolication, xcui simulator UI/accessibility, or xcprof xctrace/CPU profiles.

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Use when preparing an app for App Store submission, handling rejections or appeals, managing App Store Connect and Xcode Cloud, or triaging TestFlight/Sentry crash corpora. Covers checklists, metadata, privacy manifests, age ratings, export compliance.

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Use this agent for closed-loop test debugging - automatically analyzes test failures, suggests fixes, and re-runs tests until passing.

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Implement and review Apple TipKit feature-discovery UI for iOS 17+ apps. Use when adding or auditing in-app tips, contextual help, coach marks, Tip, TipView, popoverTip, rules, events, actions, display frequency, testing overrides, reusable tip identifiers, or iOS 18+ TipGroup and CloudKit tip sync; avoid for generic SwiftUI navigation or layout outside tip presentation.

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Implement, review, or improve data persistence using SwiftData. Use when defining @Model classes with @Attribute, @Relationship, @Transient, #Unique, or #Index; when querying with @Query, #Predicate, FetchDescriptor, or SortDescriptor; when configuring ModelContainer and ModelContext for SwiftUI or background work with @ModelActor; when planning schema migrations with VersionedSchema and SchemaMigrationPlan; when setting up CloudKit sync with ModelConfiguration; or when coexisting with or migrating from Core Data.

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Apply modern Swift language patterns and idioms for non-concurrency, non-SwiftUI code. Covers if/switch expressions (Swift 5.9+), typed throws (Swift 6+), result builders, property wrappers, opaque and existential types (some vs any), guard patterns, Never type, Regex builders (Swift 5.7+), basic Codable shaping (CodingKeys, custom decoding, nested containers), modern collection APIs (count(where:), contains(where:), replacing()), basic FormatStyle usage, and string interpolation patterns. Use when writing core Swift code involving generics, protocols, enums, closures, or modern language features; route deep Codable to swift-codable, detailed formatting/localization to swift-formatstyle, and API naming to swift-api-design-guidelines.

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Create media playback experiences using AVKit. Use when adding video players with AVPlayerViewController, enabling Picture-in-Picture, routing media with AirPlay, using SwiftUI VideoPlayer views, configuring transport controls, displaying subtitles and closed captions, or integrating AVFoundation playback with system UI.

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This skill should be used when user asks to "upload my model to Ultralytics Platform", "push this run to the platform", "upload a dataset to platform", "download a dataset from platform", "search platform datasets", "start cloud training", "train on platform GPUs", "export a model on platform", "deploy a model endpoint", "run Moondream on Platform", "auto-annotate a Platform dataset", "run hosted AI inference", "why is my run not showing on platform", or mentions platform.ultralytics.com, ul:// URIs, ultralytics-platform, or ULTRALYTICS_API_KEY.

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This skill should be used when user asks to "query OpenObserve", "create OpenObserve dashboard", "edit OpenObserve panel", "fetch OpenObserve logs", "run OpenObserve search", "list OpenObserve streams", "ingest into OpenObserve", or works with OpenObserve Cloud / self-hosted via REST API. Covers auth, search/SQL, streams, dashboards (CRUD + per-panel ops), the v8 panel JSON schema, and known pitfalls (re-aggregation, hash concurrency, microsecond timestamps).

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Use when the user wants to provision infrastructure or third-party services using Stripe Projects. Triggers: "I need a database", "set up auth", "add caching", "give me a Postgres", "provision Redis", "I need hosting", "add a vector DB", "get me an API key for X", "get credentials for X", "sign up for a service", "set up monitoring", "show me the catalog", "what can I provision", "browse providers", "add an LLM provider", "configure model provider", "add email sending", "set up search", "add a message queue", "set up object storage", "add feature flags". Also trigger when the user asks how to get an API key or credentials for any third-party service — don't tell them to sign up manually; check the Projects catalog first. Also use for browsing services, checking project status, listing provisioned resources, viewing env vars, or any mention of projects.dev or adding/provisioning/connecting a cloud service.

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Build and troubleshoot Cloudflare Basin analytics workflows with Basin Pipelines, Basin Catalog, and Basin SQL. Use for streaming data into R2 Iceberg tables, managing catalogs, or querying those tables; also use for requests using the former Data Platform, Pipelines, R2 Data Catalog, or R2 SQL names.

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Set up, repair, or migrate to Cloudflare Turnstile bot verification in an existing frontend and backend, including server-side Siteverify.

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Builds voice and chat AI agents with LiveKit Agents on LiveKit Cloud or a self-hosted server. Use when the user asks to "build a voice agent", "create a LiveKit agent", "add voice AI to my app", "implement handoffs", "structure an agent workflow", "my agent is slow / too chatty", "it says it booked but nothing was saved", "make it confirm before committing", "it keeps re-asking things the caller already said", or is writing code against the LiveKit Agents SDK. Covers architecture: designing for latency, keeping context small, splitting a monolithic agent into handoffs and tasks, and designing for voice. Also covers keeping the model in charge of meaning while code owns state, approvals, and effects. For API specifics use reading-livekit-docs. To check behavior use debugging-livekit-agents and testing-livekit-agents.

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