「ols」の検索結果

End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as screening-not-classifier (Davis 2018), tag-jumping with NovaSeq 10x MiSeq caveat (Schnell 2015), Hill-number effective species counts with coverage-based rarefaction (Jost 2006; Chao & Jost 2012; doubling rule), beta-diversity decomposition with MANDATORY PERMANOVA + PERMDISP pair (Anderson & Walsh 2013), constrained ordination, and the read-counts-not-abundance critique (Lamb 2019). Use when processing eDNA samples for biodiversity assessment, deciding ASV vs OTU, configuring OBITools3 v3, interpreting decontam screening, or reporting community comparisons with the dispersion confound check.

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End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.

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Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniverse, implement new API integrations, create tool wrappers for scientific databases/services, expand ToolUniverse capabilities, or follow ToolUniverse contribution guidelines. Supports creating tool classes, JSON configurations, validation, error handling, and test examples.

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Design tool-use patterns for AI agents. TRIGGERS - Use when user needs help with ai-agent-tools related tasks.

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Builds CARLA on Unreal Engine 5.8 from the ue58-dev branch using its CMake build system — configure a preset, then build the carla-unreal / carla-unreal-editor / carla-python-api-install / launch targets — with ROS 2, DLSS, RSS and cook-scope options, and the engine-side build of the CarlaUnreal UE 5.8 fork. There is no Makefile and no Util/BuildTools in this tree, so every UE4 `make` recipe is invalid here. Use when the user asks to "build CARLA UE5", "build ue58-dev", "compile CARLA with cmake", "rebuild the Python API", or hits a CMake configure or target failure.

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Gets a custom map into CARLA on UE 5.8 — the four distinct routes and which one to pick — via Util/Tools/Import.py for FBX+OpenDRIVE assets into a source build, CARLA_MAPS_TO_COOK to ship a map inside a package, or client.generate_opendrive_world() for an OpenDRIVE-only map at runtime with no build at all. Covers where imported assets land, why an imported map cannot be loaded from a package by name, and the four capabilities the UE4 skill has that ue58 lacks — standalone asset packages, their installer, semantic-material tagging, and a pedestrian navmesh that is generated but silently skipped. Use when the user asks to "import a map", "add a custom map", "load my .xodr", "package my own town", or "create a standalone map package".

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Controls the traffic-light actors on a running CARLA server — set a light green/red/yellow/off, freeze all lights (optionally all-green), set phase timing (green/yellow/red durations), and reset to the normal cycle. Target all lights, one by id, all in a junction, or the nearest. Use when the user asks to "make the light red", "freeze all lights green", "change the light timing", "turn the traffic lights off", or "reset the lights". This is the light actors, not the Traffic Manager (that's control-traffic).

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Controls the map's light sources through the CARLA LightManager — turn street lamps, building/facade lights, vehicle lights or all of them on/off, set their colour and intensity, and toggle the automatic lights-at-night cycle. Use when the user asks to "turn on the street lights", "light up the city at night", "turn off building lights", "change the street-light colour", or "make lights come on automatically at night". Distinct from hiding lamp meshes (toggle-env-objects) and the sun (set-weather).

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Imports an FBX vehicle into a CARLA source build as a spawnable vehicle.<make>.<model> — checks the FBX carries CARLA's 4-wheel bone rig, imports the mesh, then assembles the vehicle through CarlaTools' VehicleAuthoringLibrary (physics asset with kinematic wheel bodies, retargeted anim blueprint, four configured wheel blueprints, the vehicle blueprint), registers it in VehicleFactory through CARLA's own add_vehicle_to_vehicle_factory.py, and verifies it spawns, drives and steers. Use when the user asks to "add a car/truck/van to CARLA", "import a vehicle FBX", or needs a custom drivable vehicle spawnable from the Python API.

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Records a running CARLA simulation to a .log file via start_recorder/stop_recorder for later deterministic replay — capturing actor spawns, transforms, traffic-light states and animations (optionally velocities/controls). Use when the user asks to "record the simulation", "start/stop the recorder", "capture this run", or "save a scenario to replay later". Does NOT capture sensor images.

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Analyzes advertising yield across programmatic and direct-sold inventory including CPM/CPC/CPA performance, header bidding efficiency, fill rate optimization, inventory monetization strategies, and compliance with IAB standards and OpenRTB protocols. USE THIS SKILL WHEN: - You need to audit ad revenue performance or diagnose yield drops - Someone asks about header bidding configuration or Prebid.js optimization - You are analyzing fill rates, eCPM trends, or ad unit performance - A project involves programmatic advertising, SSP integration, or ad serving - You need to verify ads.txt, sellers.json, or supply chain compliance - Someone mentions CPM floors, bid density, or auction dynamics - You are evaluating ad quality controls, viewability, or ad-related UX impact - A codebase integrates Google Ad Manager, AdMob, Prebid, or any SSP TRIGGER PHRASES: "ad yield", "eCPM", "fill rate", "header bidding", "Prebid", "programmatic ads", "ad monetization", "CPM optimization", "ad revenue", "ads.txt", "ad serving", "SSP", "ad unit performance", "viewability"

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OpenAI API (developers.openai.com) の Responses API リファレンス。 text generation, embeddings, structured outputs, streaming, function calling, programmatic tool calling, conversation state, prompt caching, reasoning models, background mode, compaction, multi-agent。 webhooks, error codes, rate limits, Realtime API server controls。 公式 SDK (Python / JavaScript(JS) / .NET / Java / Go / Ruby), openai CLI。 Chat Completions / Assistants からの移行, deprecations。

Storybook (UI コンポーネントカタログ・テストツール) リファレンス。 story, CSF (Component Story Format)、args, argTypes, decorators、 play function、interaction tests、autodocs、 main.ts / preview.ts 設定、アドオン (a11y, controls, viewport, themes)。

React Flow (ノードベース UI / フロー図ライブラリ for React) リファレンス。 ReactFlow コンポーネント、Node, Edge, Handle, Viewport、 カスタムノード / エッジ、Controls / MiniMap / Background、 レイアウトアルゴリズム (dagre, elkjs)、ドラッグ&ドロップ、エッジ接続。

Hermes Agent CLI リファレンス。 インストール、CLI コマンド (chat, model, gateway, config, skills, cron, webhook, mcp, profile)、 Configuration (Terminal Backends, Memory, TTS / STT, Compression, Display, Auxiliary Models)、 Features (Tools, Skills, MCP, Memory, Voice Mode, Personality, Context Files)、 Messaging Gateway (14+ プラットフォーム)、Security、Architecture、 Platform Support、Nous Portal 連携 (Tool Gateway)。

OpenAI API (developers.openai.com) の Realtime API と Audio エンドポイントのリファレンス。 WebRTC / WebSocket / SIP transport, sessions / conversations / events, client secrets (ephemeral keys), VAD (server_vad / semantic_vad), tools/MCP, speech-to-speech voice agents, speech-to-text (streaming / file transcription), text-to-speech, translation。

Claude Code (code.claude.com) の拡張機能リファレンス。 Agent Skills (SKILL.md), slash commands, output styles, subagents, agent teams, agent view, workflows, routines, scheduled tasks, hooks (PreToolUse / PostToolUse), plugins, plugin marketplace, MCP 設定 (.mcp.json / claude mcp add), managed MCP, channels (--channels / claude/channel push events, webhook / telegram / discord / imessage), tools-reference, advisor, ultrareview。

Claude Agent SDK (code.claude.com/docs/en/agent-sdk) の TypeScript / Python リファレンス。 query(), ClaudeAgentOptions / Options, custom tools (in-process MCP), createSdkMcpServer, hooks, permissions (canUseTool), subagents, sessions (resume / fork), streaming, structured outputs, slash commands, tool search, hosting / observability。

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.

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Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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。