「tools」の検索結果

open Issue を triage して「次の仕事候補（N 件 + 推奨 1 件）」を窓口が人間へ提示する。 候補はオペレーターが書いたゴール台帳（registry/goals/）の条項に当たるものだけで、条項順に並ぶ。 tools/work_discovery_scan.py を 1 回実行し、その候補 JSON を 設計書 §5.2 / §12 の人間可読フォーマットでレンダリングするところで停止する（propose-only）。 起動主体は窓口に限定。手動 / イベント起動のみ（常駐 /loop なし）。 「次の仕事候補出して」「triage して」「次なにやる？」や PR マージ後の proactive next-dispatch で窓口が手動起動する。

PR の CI / マージ監視 (tools/pr-watch.sh) を broker tmux セッション内の専用ペイン pr-watch-<PR> で回す。窓口が PR 作成直後に `/pr-watch-pane <PR>` で起動すると、 ja-root cwd・sandbox 外で監視が走り、/clear や窓口セッション寿命と無関係に継続する。 pane name で冪等起動 (二重監視しない)、role=watcher で identity 登録、監視終了 (CI green / PR merged / timeout) で broker の tmux backend ならペイン自動 close (herdr / wezterm / renga のペインは tmux ペインでないため自動 close されず、窓口が 監視終端でイベント駆動 close する)。Bash tool の background は session 寿命依存で長時間 watcher には不適なので本 skill が推奨経路。 「CI 監視をペインで」「pr-watch をペインで回して」「PR <N> の CI を見張って」等で発動。

23 engineering agent skills and plugins for Claude Code, Codex, Gemini CLI, Cursor, OpenClaw, and 6 more tools. Architecture, frontend, backend, QA, DevOps, security, AI/ML, data engineering, Playwright, Stripe, AWS, MS365. 30+ Python tools (stdlib-only).

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Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks. Use when deciding bulk vs single-cell (bulk amplicon/RNA-seq -> MiXCR analyze preset -> VDJtools/immunarch depth-normalized diversity and overlap -> figures; 10x paired VDJ -> MiXCR 10x preset or Cell Ranger -> scirpy gene-expression integration, chain QC, clonotype clusters); and TCR vs BCR (TCR -> exact CDR3-nt+V/J clonotypes, VDJtools diversity is fine; BCR -> somatic hypermutation makes exact clonotypes wrong -> Immcantation distToNearest/findThreshold clonal clustering, germline reconstruction, SHM, Dowser lineages); selecting the MiXCR 4.x preset by chemistry and activating its license; downsampling to equal depth before comparing diversity or overlap; and optionally annotating antigen specificity.

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。

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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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.

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。

Stellar standards, ecosystem, and reference. Covers SEPs (Stellar Ecosystem Proposals), CAPs (Core Advancement Proposals), and a quick map for picking the right standard for wallets, anchors, payments, deposits/withdrawals, federation, deep links, and KYC. Also bundles ecosystem references (DeFi protocols, dev tools, wallets, infra, community projects), curated documentation links, and MCP servers (live tools such as Raven). Use when you need to know which SEP applies, or want a starting point for ecosystem integrations, official docs, or live MCP tooling.

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。

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

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。

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".

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。

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.

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。

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。

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)。

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。

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。

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.

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。

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.

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。

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).

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。

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.

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。

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.

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。

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。

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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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.

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。