AI Skills — Eric Yiru's Personal Library
> 112 skills for Claude Code, Codex, and AI coding agents. > Computational biology · Deep learning · Academic writing · Document automation · and more.
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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.
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Skills at a Glance
compbio (35) ████████████████████████████████████ 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 — 35 skills
Single-cell RNA-seq, spatial omics, multi-omics integration, databases, and workflow engineering.
| Category | Skills | |---------|--------| | Single-cell analysis | scanpy, seurat, scvi-tools, anndata | | H5AD interchange | anndatar, schard | | Trajectory analysis | monocle3 | | Integration | seurat-v5, harmony, scanorama, bbknn | | Visualization | cellxgene, cellxgene-census | | Spatial omics | squidpy, giotto, spatialdata, vitessce | | Platforms | visium, stereo-seq | | Multi-omics | pydeseq2, archr, signac, scribble, uniprot, metabolomics-workbench | | Databases | kegg, reactome, geo, ensembl, human-cell-atlas | | Workflows | snakemake, nextflow | | Expert workflows | draft-spatial-methods, explain-bio-dl-model, critique-bio-manuscript |
AI / ML — 12 skills
Deep learning, LLM fine-tuning, and distributed training infrastructure.
| Category | Skills | |---------|--------| | Deep learning | pytorch | | LLM ecosystem | transformers, huggingface-hub, peft, trl, bitsandbytes, cursor-usage-checker, browser-use, minimax-cli | | Training | pytorch-lightning, accelerate, datasets, deepspeed |
Programming / Python — 13 skills
Python library development from zero to production.
| Category | Skills | |---------|--------| | Foundation | project-setup, code-quality, testing-strategy, documentation | | Distribution | packaging, release-management, cli-development | | Quality | security-audit, performance, api-design, library-review, community | | Utilities | sqlite, jupyter |
Writing — 12 skills
Academic writing, literature review, LaTeX, and Obsidian knowledge management.
| Category | Skills | |---------|--------| | Academic | academic-writing-editor, humanizer, humanizer-zh | | Literature | zotpilot | | LaTeX | latex-writing, compile-latex | | Obsidian | obsidian-markdown, obsidian-cli, obsidian-bases, json-canvas, defuddle, wiki-keeper |
Documents — 19 skills
Office automation, design, and media.
| Category | Skills | |---------|--------| | Office | officecli, officecli-docx, officecli-pptx, officecli-xlsx | | Formats | docx, pptx, xlsx, pdf | | Design | frontend-design, canvas-design, theme-factory, brand-guidelines, algorithmic-art, web-artifacts-builder, webapp-testing | | Collaboration | doc-coauthoring, internal-comms | | Media | imgur-cli, slack-gif-creator |
Agents — 7 skills
Coding agents, MCP development, and behavioral guidelines.
| Category | Skills | |---------|--------| | Coding agents | claude-code, codex, hermes-agent, opencode, zed | | MCP | mcp-builder | | Guidelines | karpathy-guidelines |
Platforms — 6 skills
GitHub workflow integration.
| Category | Skills | |---------|--------| | GitHub | github-auth, github-code-review, github-issues, github-pr-workflow, github-repo-management, github-codebase-inspection |
Frontend — 2 skills
Website maintenance.
| Category | Skills | |---------|--------| | Site maintenance | page-keeper, chen-academic-page-maintainer |
Core — 4 skills
Security, performance tooling, and skill authoring.
| Category | Skills | |---------|--------| | Skill authoring | skill-creator, skill-seekers | | Security | security-audit, bitwarden |
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Workflow Bundles (Taskpacks)
Taskpacks group skills by workflow, not machine:
| Taskpack | Description | |---------|-------------| | paper-writing | Academic paper, thesis, literature review | | document-export | Office, PDF, Word, PowerPoint, Excel | | single-cell-analysis | scRNA-seq from raw reads to annotated clusters | | spatial-omics-analysis | Spatial transcriptomics — Visium, Squidpy, Giotto | | llm-finetuning | LoRA, QLoRA, RLHF, DPO fine-tuning | | pytorch-model-dev | PyTorch model development and optimization | | bio-databases | KEGG, Reactome, GEO, Ensembl, UniProt access | | workflow-engineering | Snakemake and Nextflow pipelines | | codebti | CODEBTI project bundle | | feast | Multi-omics integration — RNA, ATAC, proteomics, metabolomics | | thesis-defense | Thesis defense preparation | | zotpilot-literature-map | Literature embedding map and recommendation system |
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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, queryCore 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.
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License
MIT — see LICENSE.md