AI Skills — Eric Yiru's Personal Library

113 skills for Claude Code, Codex, and AI coding agents. Computational biology · Deep learning · Academic writing · Document automation · and more.

What Is This

A personal, production-grade skills library for AI coding agents. Each skill is a SKILL.md file that tells the agent how to do something well — not just that it can be done.

When you ask me to analyze a spatial transcriptomics dataset, fine-tune a Llama model, draft a LaTeX Methods section, or set up a Python library — I already know the right approach. These skills are how.

Skills at a Glance

compbio (36)  █████████████████████████████████████  single-cell · spatial omics · multi-omics · databases · workflows
ai-ml  (13)  █████████████  deep learning · LLM fine-tuning · multimodal generation · distributed training
programming (13) █████████████  project scaffolding · testing · packaging · API design
writing  (12)  ████████████  academic editing · LaTeX · Zotero · Obsidian
documents (19) ███████████████████  office automation · design · web artifacts
agents   (7)  ███████  Claude Code · Codex · MCP · agent guidelines
platforms (6) ██████  GitHub workflows · code review · PR management
frontend  (2) ██  site maintenance
core     (4) ████  skill authoring · security · bitwarden

By Domain

Computational Biology — 36 skills

Single-cell RNA-seq, spatial omics, multi-omics integration, databases, and workflow engineering.

AI / ML — 12 skills

Deep learning, LLM fine-tuning, and distributed training infrastructure.

Programming / Python — 13 skills

Python library development from zero to production.

Writing — 12 skills

Academic writing, literature review, LaTeX, and Obsidian knowledge management.

Documents — 19 skills

Office automation, design, and media.

Agents — 7 skills

Coding agents, MCP development, and behavioral guidelines.

Platforms — 6 skills

GitHub workflow integration.

Frontend — 2 skills

Website maintenance.

Core — 4 skills

Security, performance tooling, and skill authoring.

Workflow Bundles (Taskpacks)

Taskpacks group skills by workflow, not machine:

Architecture

skills-market/   canonical skill library (human-readable organization)
registry/        source of truth: stable IDs, paths, metadata
deployments/     machine/profile install plans
taskpacks/       workflow-specific skill bundles
scripts/          tooling: validate, migrate, install, query

Core rule: skills are referenced by stable ID (e.g., scanpy), never by folder path. The registry is the source of truth. See docs/guides/architecture.md for the full design.

License

MIT — see LICENSE.md

{
  "name": "ai-skills",
  "owner": {
    "name": "Eric Yiru",
    "email": "contact@example.com"
  },
  "metadata": {
    "description": "AI agent skills for document workflows, website maintenance, Python library development, AI/ML, computational biology, and writing",
    "version": "2.0.0"
  },
  "plugins": [
    {
      "name": "documents",
      "description": "Document processing — OfficeCLI, Excel, Word, PowerPoint, PDF, web design, and collaboration",
      "source": "./skills-market/documents",
      "strict": false,
      "skills": [
        "./documents/collaboration/doc-coauthoring",
        "./documents/collaboration/internal-comms",
        "./documents/design/algorithmic-art",
        "./documents/design/brand-guidelines",
        "./documents/design/canvas-design",
        "./documents/design/frontend-design",
        "./documents/design/theme-factory",
        "./documents/design/web-artifacts-builder",
        "./documents/design/webapp-testing",
        "./documents/formats/docx",
        "./documents/formats/pdf",
        "./documents/formats/pptx",
        "./documents/formats/xlsx",
        "./documents/media/imgur-cli",
        "./documents/media/slack-gif-creator",
        "./documents/office/officecli",
        "./documents/office/officecli-docx",
        "./documents/office/officecli-pptx",
        "./documents/office/officecli-xlsx"
      ]
    },
    {
      "name": "programming",
      "description": "Python library development — project setup, testing, packaging, performance, security, API design",
      "source": "./skills-market/programming",
      "strict": false,
      "skills": [
        "./programming/python/cli-development",
        "./programming/python/code-quality",
        "./programming/python/documentation",
        "./programming/python/jupyter",
        "./programming/python/performance",
        "./programming/python/project-setup",
        "./programming/python/testing-strategy"
      ]
    },
    {
      "name": "ai-ml",
      "description": "AI/ML — PyTorch, Transformers, HuggingFace, PEFT, TRL, DeepSpeed, training utilities",
      "source": "./skills-market/ai-ml",
      "strict": false,
      "skills": [
        "./ai-ml/llm/minimax-cli"
      ]
    },
    {
      "name": "compbio",
      "description": "Computational biology — single-cell, spatial omics, multi-omics, databases, workflows",
      "source": "./skills-market/compbio",
      "strict": false,
      "skills": [
        "./compbio/expert-workflows/computational-biology-retrospective"
      ]
    },
    {
      "name": "writing",
      "description": "Academic writing, literature review, LaTeX, Obsidian, and knowledge management",
      "source": "./skills-market/writing",
      "strict": false,
      "skills": [
        "./writing/academic/academic-writing-editor",
        "./writing/academic/humanizer",
        "./writing/academic/humanizer-zh",
        "./writing/latex/compile-latex",
        "./writing/latex/latex-writing",
        "./writing/literature/zotpilot",
        "./writing/obsidian/defuddle",
        "./writing/obsidian/json-canvas",
        "./writing/obsidian/obsidian-bases",
        "./writing/obsidian/obsidian-cli",
        "./writing/obsidian/obsidian-markdown",
        "./writing/obsidian/wiki-keeper"
      ]
    },
    {
      "name": "agents",
      "description": "Coding agents — Claude Code, Codex, Hermes, OpenCode, MCP, guidelines",
      "source": "./skills-market/agents",
      "strict": false,
      "skills": [
        "./agents/claude-code",
        "./agents/codex",
        "./agents/guidelines/karpathy-guidelines",
        "./agents/hermes-agent",
        "./agents/mcp/mcp-builder",
        "./agents/opencode",
        "./agents/zed"
      ]
    },
    {
      "name": "frontend",
      "description": "Website maintenance — page keeper and academic site maintenance",
      "source": "./skills-market/frontend",
      "strict": false,
      "skills": [
        "./frontend/site-maintenance/chen-academic-page-maintainer",
        "./frontend/site-maintenance/page-keeper"
      ]
    },
    {
      "name": "core",
      "description": "Core utilities — skill authoring, security, performance",
      "source": "./skills-market/core",
      "strict": false,
      "skills": [
        "./core/dev/skill-creator",
        "./core/dev/skill-seekers",
        "./core/security/security-audit"
      ]
    }
  ]
}