Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling.
EnglishExecute AI-generated code in secure isolated E2B cloud sandboxes with advanced monitoring, MCP gateway integration (200+ tools), and multi-language support. Use for running Python/JavaScript/TypeScript/Bash code, managing sandbox lifecycle (create, pause, resume, kill, list, connect), monitoring metrics (CPU, memory, disk), handling lifecycle events, uploading/downloading files, streaming command output, environment variable management, and integrating LLMs with code execution capabilities.
EnglishGitHub Actions CI/CD guide for the dotfiles repository. Use when creating or modifying GitHub Actions workflows, adding CI/CD pipelines, setting up build/test automation, configuring matrix builds, working with artifacts, implementing E2E tests in containers, or troubleshooting workflow issues. Covers workflow patterns, security best practices, caching strategies, and multi-platform testing.
EnglishAbility to analyse, design, optimise, and improve systems that integrate people, processes, technology, and resources to meet defined performance, quality, cost, and safety requirements. Includes applying engineering, statistical, and systems methods to model workflows, identify inefficiencies, evaluate trade-offs, and implement improvements across operations and supply chains. Applies across manufacturing, services, logistics, healthcare, and infrastructure contexts and is independent of specific tools or industries, with human accountability retained for decisions, outcomes, and impacts.
EnglishBuild comprehensive ML pipelines, experiment tracking, and model registries with MLflow, Kubeflow, and modern MLOps tools.
EnglishStandardized report structure, recommendations, and reportlab PLATYPUS patterns for all Biotrackr health…
EnglishUse when implementing data analysis pipelines, statistical tests, or bioinformatics workflows in code (Python/R), particularly for genomics, transcriptomics, proteomics, or other -omics data.
Latin
AGENT SKILLS ATLASIncludes Bio Single Cell Cell Annotation, Bio Workflows Gwas Pipeline, Cell Detection, and other workflows.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLISupported by the Atlas install prompt. Skill-specific requirements vary.
Pack stats
What’s included
Bio Single Cell Cell Annotation
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. Use when autom
Bio Workflows Gwas Pipeline
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative trait
Cell Detection
Cell segmentation in fluorescence microscopy images. Supports Cellpose/cpsam (Cellpose 4.0) with additional backends
E2b Sandbox
Execute AI-generated code in secure isolated E2B cloud sandboxes with advanced monitoring, MCP gateway integration (200+ tools), and multi-language support. Use for running Python/JavaScript/TypeScript/Bash code, managing sandbox lifecycle (create, pause, resume, kill, list, connect), monitoring metrics (CPU, memory, disk), handling lifecycle events, uploading/downloading files, streaming command output, environment variable management, and integrating LLMs with code execution capabilities.
GitHub Actions CI
GitHub Actions CI/CD guide for the dotfiles repository. Use when creating or modifying GitHub Actions workflows, adding CI/CD pipelines, setting up build/test automation, configuring matrix builds, working with artifacts, implementing E2E tests in containers, or troubleshooting workflow issues. Covers workflow patterns, security best practices, caching strategies, and multi-platform testing.
Industrial Engineer
Ability to analyse, design, optimise, and improve systems that integrate people, processes, technology, and resources to meet defined performance, quality, cost, and safety requirements. Includes applying engineering, statistical, and systems methods to model workflows, identify inefficiencies, evaluate trade-offs, and implement improvements across operations and supply chains. Applies across manufacturing, services, logistics, healthcare, and infrastructure contexts and is independent of specific tools or industries, with human accountability retained for decisions, outcomes, and impacts.
Mlops Engineer
Build comprehensive ML pipelines, experiment tracking, and model registries with MLflow, Kubeflow, and modern MLOps tools.
Report Template
Standardized report structure, recommendations, and reportlab PLATYPUS patterns for all Biotrackr health reports
Bioinformatician
Use when implementing data analysis pipelines, statistical tests, or bioinformatics workflows in code (Python/R), particularly for genomics, transcriptomics, proteomics, or other -omics data.
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Use the Bio Single Cell Cell Annotation skill to help with my task.
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