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

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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, 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.

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License

MIT — see LICENSE.md