「dex」の検索結果

Reflective pass over your memory files — merge duplicates, fix stale facts, prune the index.

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Search, create, and manage notes in the Obsidian vault with wikilinks and index notes. Use when user wants to find, create, or organize notes in Obsidian.

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Design database schemas — tables, relationships, indexes, constraints, and ORM setup. Covers relational design, normalization, and common patterns.

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Facebook's library for efficient similarity search and clustering of dense vectors. Supports billions of vectors, GPU acceleration, and various index types (Flat, IVF, HNSW). Use for fast k-NN search, large-scale vector retrieval, or when you need pure similarity search without metadata. Best for high-performance applications.

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Builds and validates predictive time-to-event models on clinical and omics data with penalized Cox, random survival forests, gradient-boosted and deep survival models, and prediction-grade evaluation (Uno's C, time-dependent AUC, integrated Brier, calibration, competing risks). Use when building an individualized risk predictor or prognostic omics signature, choosing a survival model, or evaluating one beyond the C-index. For Kaplan-Meier, log-rank, and classical Cox hazard-ratio inference in a trial see clinical-biostatistics/survival-analysis.

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Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on Toil/Arvados/Calrissian. Use when deciding CWL (portability/provenance/regulated) vs Nextflow/WDL/Snakemake; declaring secondaryFiles for indexed companions (.bai/.fai/.dict/.tbi and the caret rule); putting resources/containers under requirements (must-hold) vs hints (advisory) to avoid silent OOM; choosing scatterMethod (dotproduct vs flat_/nested_crossproduct); preferring $(...) parameter refs over ${...} JavaScript for portability; pinning DockerRequirement images; or emitting a CWLProv provenance object for audited/clinical settings.

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This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

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Detect and auto-install missing ToolUniverse research skills. Checks common Claude Code/Cursor/Codex skill directories for the canary file, and installs any missing skills if none found. Use when the plugin's research skills aren't loading, when migrating between clients, or when verifying a skill installation.

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End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/beta diversity at a declared sampling depth (phyloseq/vegan, adonis2 paired with betadisper), compositional DA as a consensus of >=2 tools (ALDEx2/ANCOM-BC2) on unrarefied counts, and optional PICRUSt2 functional prediction gated on NSTI. Covers the stage-ordering decisions (primers before truncation, per-run error model, rarefy for diversity not DA, predicted potential not activity) and defers each per-step choice to the six microbiome skills. Use when staging an amplicon study end to end or chaining ASV inference, taxonomy, diversity, and differential abundance. For shotgun reads see workflows/metagenomics-pipeline.

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Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Trae, Cline, etc.), full CLI reference (tu list/grep/find/info/run/test/status/build/serve), Coding API quickstart, agentic tools, code executor, API key walkthrough, skill installation, and upgrading. Use when user asks how to set up ToolUniverse, which access mode to use (MCP vs CLI vs SDK), configuring MCP servers, using the CLI, troubleshooting installation, upgrading, or mentions installing ToolUniverse or setting up scientific tools. Also triggers for "how do I use ToolUniverse", "what's the best way to access tools", "command line", "tu command", "coding API", "tu build".

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End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comprehensive splicing analysis from raw bulk RNA-seq data; for variant-driven splice prediction see splice-variant-prediction; for rare-disease single-patient outlier detection see outlier-splicing-detection; for full-isoform PacBio/ONT analysis see long-read-splicing.

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Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference models (Bliss independence, HSA / highest single agent, Loewe additivity, ZIP, and the Chou-Talalay Combination Index). Use when you have measured single-drug and combination effects (inhibition/viability) and need a synergy score. Explains which model to use, what data each one needs, and how to read the score. NOT for looking up pre-computed synergy in a database (use the SYNERGxDB tool / cell-line-profiling skill).

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Use to process automated PR review feedback (Copilot, Greptile, Codex) and iterate until all AI threads are addressed, checks are green, and the PR is merge-ready. Trigger when the user says "address review feedback", "recycle reviews", or references an automated reviewer.

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Use every time you push a commit to an active pull request, to verify the PR is truly stable before reporting merge readiness. Covers the post-push wait window, AI review audit (Copilot/Greptile/Codex), and the gh commands to snapshot PR state. Trigger on "I pushed" or "is the PR ready to merge".

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Configure and debug MCP servers for OpenCode, Codex CLI, and Claude Code, including auth headers, scope, and validation checks. Use when MCP tools fail to connect or when adding a new MCP server.

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Configure and debug MCP servers for Claude Code, OpenCode, and Codex CLI, including auth headers, scope, and validation checks. Use when MCP tools fail to connect, when an MCP server returns 401/404/HTML, or when adding a new MCP server to this repo.

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Querying Stellar chain data via Stellar RPC (preferred) and Horizon (legacy). Covers RPC JSON-RPC methods, Horizon REST endpoints, streaming, pagination, historical queries, Hubble/Galexie for deep history, and the RPC/Horizon migration story. Use when reading balances, transactions, operations, ledgers, contract events, or building any indexer/analytics workflow.

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Answers "can CARLA do X here, and is there a vetted procedure for it" before you promise anything, and detects client/server/tree version skew — a support matrix over the whole collection (covered by a skill / works but undocumented / present but untested / broken or removed), an index of the features that are verified BROKEN on 0.10.0 (gbuffers crash the server, map layers do nothing, Landmark.waypoint is None, standalone asset packages are gone), and a probe that reports what this machine's build flags and running server actually offer. Use when the user asks whether CARLA supports something, when a feature has no skill, when a UE4 tutorial's steps do not exist, or before improvising a procedure.

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Audit and improve website readiness for AI agents using the Cloudflare "Is It Agent Ready?" scanner (isitagentready.com). Covers scanning via API, interpreting results, generating implementation prompts, and fixing every check. Use when the user mentions "agent ready", "isitagentready", "AI agent scan", "agent readiness", "agent-ready score", "MCP server card", "agent skills index", "markdown for agents", "content signals", "web bot auth", "agent discovery", "RFC 9727", "RFC 8288", "RFC 9728", "SEP-1649", "WebMCP", "x402", "UCP", "ACP", or wants to make a website discoverable and usable by AI agents.

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MUST USE for building FastAPI/REST API applications with Aerospike database (aerospike-py Rust/PyO3 async client). Covers AsyncClient lifespan management, FastAPI Depends injection, aerospike_py exception-to-HTTP-status mapping (RecordNotFound→404, RecordExistsError→409, BackpressureError→503, AerospikeTimeoutError→504), POLICY_EXISTS_CREATE_ONLY/UPDATE_ONLY for CRUD semantics, NamedTuple attribute access (record.bins not tuple unpacking), client.ping() readiness probe, batch_read returning dict, batch_write with in_doubt retry signal, and global AerospikeError handler. Triggers on: FastAPI + Aerospike, REST API + aerospike-py, CRUD API with Aerospike, client.ping() health probe, batch_read/batch_write endpoint, web server/HTTP service backed by Aerospike NoSQL, uvicorn + Aerospike.

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Audit agent configuration files for security vulnerabilities and misconfigurations. Covers settings.json, .mcp.json, .codex/config.toml, AGENTS.md, hooks, plugin manifests, and relay config. Classify findings as P0 or P1.

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Design, audit, and improve accessibility and inclusive user experiences. Use when Codex is asked about WCAG, keyboard navigation, focus states, screen readers, ARIA, contrast, captions, reduced motion, forms, semantic HTML, accessible UI, game accessibility, inclusive design, accessibility QA, or compliance-sensitive accessibility work.

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Creates, debugs, and optimizes GitHub Actions workflow YAML files. Recommends current action versions with SHA pinning from a daily-updated index of 120+ actions. Configures matrix builds, dependency caching, reusable workflows, OIDC authentication, secrets management, and runner selection. Reviews existing workflows for outdated actions, security issues, and performance problems. Use when the user asks about GitHub Actions, workflows, CI/CD, .github/workflows, any action by name (actions/checkout, setup-node, setup-python, etc.), or workflow optimization.

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Use when working with access policies, field access, authorization middleware, gates, route access control, AccessResult semantics, permission handlers, or files in packages/access/, packages/routing/src/AccessChecker.php, packages/user/src/Middleware/. Covers entity-level access (deny-by-default via isAllowed), field-level access (open-by-default via !isForbidden), the Gate system, route options (_public, _permission, _role, _gate), and the SessionMiddleware/AuthorizationMiddleware pipeline in public/index.php.

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。