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概要と使いどころ
scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.
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Python library for genomic interval ML. Train/apply region2vec embeddings turning BED regions into vectors, index interval datasets for ML, search embedding space with BEDSpace, and evaluate embedding quality. Use for chromatin accessibility clustering, regulatory element classification, and cross-sample region comparison.
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Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS, Golden Triangle, Ro3), structural alerts (PAINS, NIBR, Lilly Demerits), chemical group detectors, complexity metrics, and filter composition query language. Built on RDKit/datamol. For hit-to-lead filtering, library design, ADMET pre-screening. For molecular I/O use rdkit-cheminformatics or datamol.
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Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve with NSGA-II, NSGA-III, MOEA/D, GAs, or differential evolution. Analyze Pareto fronts, visualize trade-offs, customize operators and callbacks. For engineering design, hyperparameter search, and conflicting objectives. Alternatives: scipy.optimize (single-objective, gradient), platypus, jMetalPy (Java).
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Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric ops (buffer, simplify, centroid, affine), spatial analysis (joins, overlays, dissolve, clipping, distance), visualization (choropleth, interactive maps, basemaps). Use for spatial joins, overlays, CRS transforms, area/distance, maps.
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NEJM figure preparation: resolution (300-1200 DPI), editable vector formats (AI/EPS/SVG), in-house medical illustration policy, and strict image integrity requirements.
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Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis. 2D/3D with subpixel accuracy; reads TIF stacks, AVI, image series via pims. Use for quantitative SPT and diffusion coefficient extraction from fluorescence or brightfield video.
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3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.
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Assemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from already-rendered panels the user supplies (PNG/PDF). Ask the user to pick one of two approaches: (1) redraw every panel into one unified figure using independent, tightly packed `subfigures` (each sized to its own labels, so axes need NOT align), consistent style, correctly placed panel letters, and per-panel legends/colorbars; (2) composite already-rendered PNG/PDF panels onto a mosaic canvas and add panel letters (image compositing, not plotting). Both export vector PDF + high-DPI PNG. For a SINGLE plot from a data table, use the sibling `omics-plotting` skill instead.
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Master advanced AgentDB features including QUIC synchronization, multi-database management, custom distance metrics, hybrid search, and distributed systems integration. Use when building distributed AI systems, multi-agent coordination, or advanced vector search applications.
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Create new Claude Code Skills with proper YAML frontmatter, progressive disclosure structure, and complete directory organization. Use when you need to build custom skills for specific workflows, generate skill templates, or understand the Claude Skills specification.
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Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations. Use when optimizing memory usage, improving search speed, or scaling to millions of vectors.
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Consolidate IBRK trade CSV files from a directory into a summary report. Groups trades by symbol, underlying, date, strike, buy/sell, and open/close. Outputs both markdown and CSV.
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Testing strategies, patterns, and tools for robotics software. Use this skill when writing unit tests, integration tests, simulation tests, or hardware-in-the-loop tests for robot systems. Trigger whenever the user mentions testing ROS nodes, pytest with ROS, launch_testing, simulation testing, CI/CD for robotics, test fixtures for sensors, mock hardware, deterministic replay, regression testing for robot behaviors, or validating perception/planning/control pipelines. Also covers property-based testing for kinematics, fuzz testing for message handlers, and golden-file testing for trajectories.
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Persistent compounding memory for AI agents. 5 default MCP tools: session_start, session_end, remember, recall, check. Full surface: 6 tools with --full (adds check_action); 13 tools with AR_EXTRAS=1 --full. Two-verb model: inhale (session_start) and exhale (session_end). Correction-first memory with decision trail tracking, watch_for warnings, palace rooms with salience scoring, cross-project insight matching, same-day journal merging, ambient recall hooks. Local markdown only. Zero cloud, zero telemetry, Obsidian-compatible. Optional Supabase backend: when configured via `ar setup supabase`, recall() uses pgvector cosine similarity on OpenAI/Voyage embeddings instead of keyword search — same API, semantic understanding. Gracefully degrades to local search if not configured.
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Provides AWS CloudFormation patterns for Amazon Bedrock resources including agents, knowledge bases, data sources, guardrails, prompts, flows, and inference profiles. Use when creating Bedrock agents with action groups, implementing RAG with knowledge bases, configuring vector stores, setting up content moderation guardrails, managing prompts, orchestrating workflows with flows, and configuring inference profiles for model optimization.
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Implements document chunking, embedding generation, vector storage, and retrieval pipelines for Retrieval-Augmented Generation systems. Use when building RAG applications, creating document Q&A systems, or integrating AI with knowledge bases.
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Provides Retrieval-Augmented Generation (RAG) implementation patterns with LangChain4j for Java. Generates document ingestion pipelines, embedding stores, vector search, and semantic search capabilities. Use when building chat-with-documents systems, document Q&A over PDFs or text files, AI assistants with knowledge bases, semantic search over document repositories, or knowledge-enhanced AI applications with source attribution.
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Provides chunking strategies for RAG systems. Generates chunk size recommendations (256-1024 tokens), overlap percentages (10-20%), and semantic boundary detection methods. Validates semantic coherence and evaluates retrieval precision/recall metrics. Use when building retrieval-augmented generation systems, vector databases, or processing large documents.
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Detect anomalies and outliers in construction data: unusual costs, schedule variances, productivity spikes. Statistical and ML-based detection methods.
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Semantic search in the DDC CWICR construction cost database using vector embeddings (BGE-M3, 1024-dim, per-language Qdrant collections). Find similar work items and resources for cost estimation across 8 national bases and 30 markets in 26 languages.
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Automated cost estimation from BIM models using DDC CWICR database (8 national bases, 78,228 positions). AI classification + vector search for accurate pricing.
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Train ML models on Databricks. Use for: classification/regression/deep-learning (XGBoost, scikit-learn, LightGBM, PyTorch) with Optuna, @prod/@challenger aliases, batch scoring (spark_udf for plain models, fe.score_batch for feature-store-backed), custom PyFunc, custom ResponsesAgent (LangGraph + UC Function/Vector Search); UC feature tables + FeatureLookup + point-in-time joins + Lakebase online store; declarative Feature Views (create_feature, DeltaTableSource, RollingWindow/SlidingWindow/TumblingWindow, materialize_features, streaming Kafka features). NOT for: endpoint ops (databricks-model-serving), MLflow evaluation (databricks-mlflow-evaluation).
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Python backend for Databricks Apps — FastAPI (default), Flask, Dash, Streamlit, Gradio, Reflex. **Default for a new Databricks App is `databricks-apps` (AppKit — Node/TypeScript/React) — reach for it first.** Use this skill only when the user asks for a Python backend, extends an existing Python app, or the team is Python-only. Covers OAuth auth, app resources, SQL warehouse and Lakebase connectivity, foundation-model / Vector Search / model-serving APIs (via `databricks-python-sdk`), and deployment via CLI or DABs.
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。