oimiragieo
- 991 skills
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- ▌ Pdb Database · oimiragieo bundleAccess RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
- ▌ PPTX Posters · oimiragieo bundleCreate research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.
- ▌ Auto Recall · oimiragieo bundleUse when you need semantic retrieval from perpetual memory at query time. Parses query intent, searches vector store, ranks by relevance and recency, and injects context. Complements memory-search.cjs with the perpetual_memory LanceDB table.
- ▌ Cron Runner · oimiragieo bundleBackground orchestrator that drains the system-wide cron-actions-queue.jsonl queue safely, preventing LLM context pollution in the primary router.
- ▌ Data Expert · oimiragieo bundleData processing expert including parsing, transformation, and validation
- ▌ De Sloppify · oimiragieo bundleTwo-agent cleanup pattern. Implementer works freely, then a dedicated cleanup agent removes unused imports, console.logs, commented-out code, dead code, and formatting issues. Produces a diff of what was cleaned.
- ▌ Exa Monitor · oimiragieo bundleScheduled Exa web search monitor. Uses CronCreate to search configured topics every 4 hours via mcp__Exa__web_search_exa, deduplicates URLs via MemoryRecord, and stores summaries for morning briefing integration.
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- ▌ Huggingface · oimiragieo bundleHugging Face Hub operations, model inference, dataset management, PEFT/LoRA fine-tuning, and Spaces deployment via MCP tools and Python APIs
- ▌ Java Expert · oimiragieo bundleJava and Spring Boot expert including REST APIs, JPA, and microservices
- ▌ LLM Council · oimiragieo bundleOrchestrate multi-LLM parallel debate and synthesis. Dispatches prompts to available omega CLI wrappers in parallel, collects independent responses, runs anonymized peer review ranking, and synthesizes via a chairman model. Supports collaboration templates, idle watchdog, inter-agent messaging, worktree isolation, and multi-turn sessions. No server required.
- ▌ MCP Builder · oimiragieo bundleGuide developers in creating Model Context Protocol (MCP) servers. Use for building MCP tools that enable LLMs to interact with external services. Covers TypeScript (primary) and Python FastMCP (secondary), tool annotations, Zod/Pydantic validation, and evaluation question creation.
- ▌ Go Expert · oimiragieo bundleGo programming expert including APIs, gRPC, concurrency, and best practices
- ▌ Heartbeat · oimiragieo bundleStart and manage the full heartbeat ecosystem for agent-studio. Registers all 7 heartbeat loops plus auto-reschedule task via CronCreate to keep the agent ecosystem healthy, indexed, informed, and connected.
- ▌ Linear Pm · oimiragieo bundleLinear project management - issues, projects, cycles, and roadmaps. Use for Linear-related tasks like managing issues, tracking sprints, and organizing projects.
- ▌ Shadcn UI · oimiragieo bundleDeep expertise on shadcn/ui component library including installation, customization, theming, and accessibility patterns. Use when building UI with shadcn/ui components, integrating Radix UI primitives, configuring Tailwind CSS v4 themes, or implementing dark mode. Covers Next.js App Router, Pages Router, and Vite setups.
- ▌ Spec Init · oimiragieo bundleUnified skill that guides spec creation through structured, interactive process.
- ▌ Assimilate · oimiragieo bundleBenchmark external agent frameworks, auto-detect source type, scan for prompt injection, and convert findings into a concrete TDD upgrade backlog for agent-studio evolution.
- ▌ Claude API · oimiragieo bundleBuild apps with the Claude API or Anthropic SDK. TRIGGER when: code imports `anthropic`/`@anthropic-ai/sdk`/`claude_agent_sdk`, or user asks to use Claude API, Anthropic SDKs, or Agent SDK. DO NOT TRIGGER when: code imports `openai`/other AI SDK, general programming, or ML/data-science tasks.
- ▌ Filesystem · oimiragieo bundleFile system operations guidance - read, write, search, and manage files using Claude Code's built-in tools.
- ▌ Fix Review · oimiragieo bundleVerify fix commits address security findings without introducing new bugs or regressions. Analyzes diffs for anti-patterns like removed validation, weakened access control, reduced error handling, reordered external calls, and changed integer operations. Generates structured FIX_REVIEW_REPORT with finding status tracking.
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- ▌ Markitdown · oimiragieo bundleConvert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
- ▌ Matplotlib · oimiragieo bundleLow-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.
- ▌ Pylabrobot · oimiragieo bundleVendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.
- ▌ Scikit Bio · oimiragieo bundleBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
- ▌ Scvi Tools · oimiragieo bundleDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
- ▌ Umap Learn · oimiragieo bundleUMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
- ▌ Bioservices · oimiragieo bundleUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
- ▌ Paper 2 Web · oimiragieo bundleThis skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.
- ▌ Git Expert · oimiragieo bundleAdvanced Git operations wrapper. Optimizes token usage by guiding complex git workflows into efficient CLI commands.
- ▌ Github MCP · oimiragieo bundleGitHub API operations - repositories, issues, pull requests, actions, code security, discussions, gists, and more. Use for GitHub-related tasks like managing PRs, issues, searching code, and monitoring workflows.
- ▌ Github Ops · oimiragieo bundleWorkflow for repository reconnaissance and operations using GitHub CLI (gh). Optimizes token usage by using structured API queries instead of blind file fetching.
- ▌ IOS Expert · oimiragieo bundleiOS development expert including SwiftUI, UIKit, and Apple frameworks
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- ▌ Ralph Loop · oimiragieo bundleAutonomous iteration loop with dual-mode support. Standalone mode uses Stop hooks (RALPH_ACTIVE=1). Multi-agent mode uses router-managed iteration. Never traps the host/router session.
- ▌ Uat Verify · oimiragieo bundleVerify completed work against acceptance criteria, collect evidence, and produce a PASS/FAIL UAT report
- ▌ Vue Expert · oimiragieo bundleVue.js ecosystem expert including Vue 3, Composition API, Nuxt, and Pinia
- ▌ API Testing · oimiragieo bundleAPI security testing and validation for REST/GraphQL/gRPC endpoints, contract testing, load testing, fuzzing, and Postman/Bruno/Hurl workflows
- ▌ Hypogenic · oimiragieo bundleAutomated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.
- ▌ Neurokit2 · oimiragieo bundleComprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
- ▌ Pennylane · oimiragieo bundleHardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
- ▌ Pufferlib · oimiragieo bundleHigh-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.
- ▌ Torchdrug · oimiragieo bundlePyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.
- ▌ Strict User Requirements Adherence · oimiragieo bundleStrictly adheres to specified user flow and game rules, making sure to follow documented features.
- ▌ Fiber Logging And Project Structure · oimiragieo bundleApplies best practices for logging (zerolog/zap), project structure (cmd/internal/pkg), middleware registration order, and environment configuration in Go Fiber v2/v3 applications.
- ▌ Etetoolkit · oimiragieo bundlePhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
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- ▌ Tdd · oimiragieo bundleCanon TDD for humans and AI agents. Use for production code changes by writing tests first, proving RED, implementing minimal GREEN, and refactoring safely. 2026 edition adds TDP, flakiness gate, ralph-loop integration, memory-search in Step 0, PBT as Step 5.5, mutation testing gate in Step 4, and CJS LSP warning.
- ▌ Init · oimiragieo bundleAuto-evolution skill to initialize a new repository with AGENTS.md localized context.
- ▌ PPTX · oimiragieo bundlePowerPoint presentation generation using python-pptx. Create slides from Claude output, data analysis, or structured content. Covers slide templates, shapes, charts, tables, and themed presentations. Use for generating .pptx files programmatically.
- ▌ XLSX · oimiragieo bundleExcel spreadsheet generation using openpyxl and xlsxwriter. Convert Claude output, data analysis results, and tabular data into formatted .xlsx files with charts, formulas, conditional formatting, and multiple sheets. Use for generating Excel reports programmatically.
- ▌ Figma · oimiragieo bundleFigma design-to-code workflow. Read Figma files, inspect components, extract design tokens, and translate designs to implementation. Use when working with Figma designs, extracting styles, or building design systems.
- ▌ Pymatgen · oimiragieo bundleMaterials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
- ▌ Pyopenms · oimiragieo bundleComplete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
- ▌ Function Length And Responsibility · oimiragieo bundleThis rule enforces the single responsibility principle, ensuring functions are short and focused.
- ▌ Interactive Requirements Gathering · oimiragieo bundleStructured interactive questionnaire framework for gathering requirements from users. Uses A/B/C/D/E multiple choice patterns with additive vs exclusive question classification.
- ▌ Multi Agent Architecture Reference · oimiragieo bundleDecision matrix for selecting multi-agent topologies (Supervisor, Swarm, Hierarchical, Conductor) with token economics, failure modes, and escalation paths
- ▌ Biopython · oimiragieo bundleComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
- ▌ Deeptools · oimiragieo bundleNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
- ▌ Geopandas · oimiragieo bundlePython library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
- ▌ Medusa · oimiragieo bundleMedusa v2 rules and best practices for modular commerce architecture, Workflow SDK, data models, services, and admin customizations.
- ▌ Readme · oimiragieo bundleUse when creating, updating, or generating README and documentation files for projects and libraries
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- ▌ Ripgrep · oimiragieo bundleEnhanced code search with custom ripgrep binary supporting ES module extensions and advanced patterns.
- ▌ Recovery · oimiragieo bundleWorkflow recovery protocol for resuming workflows after context loss, session interruption, or errors. Handles state reconstruction, artifact recovery, and seamless workflow continuation.
- ▌ Web Perf · oimiragieo bundleStructured 5-phase web performance audit workflow with Core Web Vitals thresholds and actionable optimization recommendations. Use when auditing website performance, diagnosing slow page loads, optimizing Core Web Vitals scores, or reviewing frontend performance patterns. Covers Webpack, Vite, Next.js, and Nuxt optimization.
- ▌ Arxiv MCP · oimiragieo bundleSearch and retrieve academic papers from arXiv.org using WebFetch and Exa. No MCP server required - uses existing tools to access arXiv API directly.
- ▌ Cloud Run · oimiragieo bundleGoogle Cloud Run deployment, service management, traffic splitting, and log inspection. Use when deploying containerized apps to Cloud Run, managing services, or inspecting Cloud Run logs.
- ▌ Debugging · oimiragieo bundleSystematic 4-phase debugging with root cause investigation. Use when fixing bugs to prevent random fixes.
- ▌ Datamol · oimiragieo bundlePythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
- ▌ Denario · oimiragieo bundleMultiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
- ▌ Lamindb · oimiragieo bundleThis skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
- ▌ Matchms · oimiragieo bundleSpectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
- ▌ Medchem · oimiragieo bundleMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
- ▌ Molfeat · oimiragieo bundleMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
- ▌ Pydicom · oimiragieo bundlePython library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
- ▌ Seaborn · oimiragieo bundleStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualization.
- ▌ Fiber Routing And Csrf Protection · oimiragieo bundleFocuses on routing, CSRF protection, context handling, and template usage within the internal handlers directory.
- ▌ Arboreto · oimiragieo bundleInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
- ▌ Deepchem · oimiragieo bundleMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
- ▌ Diffdock · oimiragieo bundleDiffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
- ▌ Fluidsim · oimiragieo bundleFramework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
- ▌ Histolab · oimiragieo bundleLightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
- ▌ Networkx · oimiragieo bundleComprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
- ▌ Pydeseq2 · oimiragieo bundleDifferential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
- ▌ Pyhealth · oimiragieo bundleComprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).
- ▌ Qiskit · oimiragieo bundleIBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
- ▌ Scanpy · oimiragieo bundleStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
- ▌ Tauri Svelte Typescript General · oimiragieo bundleGeneral rules for developing desktop applications using Tauri with Svelte and TypeScript for the frontend.
- ▌ Poetry Rye Dependency Management · oimiragieo bundlePython dependency management with Poetry and Rye -- lockfile-driven workflows, dependency groups, monorepo patterns, and migration paths. Covers pyproject.toml-centric packaging for projects not yet on uv.
- ▌ Adaptyv · oimiragieo bundleCloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
- ▌ Anndata · oimiragieo bundleData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
- ▌ Astropy · oimiragieo bundleComprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
- ▌ Cobrapy · oimiragieo bundleConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
- ▌ Ask Questions If Underspecified · oimiragieo bundleAsk the minimum clarifying questions before implementation when requirements are ambiguous or missing crucial details
- ▌ Jupyter Notebook Best Practices · oimiragieo bundleGuidelines for structuring and documenting Jupyter notebooks for reproducibility and clarity.
- ▌ Prioritize Python 3 10 Features · oimiragieo bundlePrioritizes the use of new features available in Python 3.12 and later versions.
- ▌ Flowio · oimiragieo bundleParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
- ▌ Geniml · oimiragieo bundleThis skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.