面向计算生物学的标准 Agent Skills 工具库 —— 遵循 Agent Skills 开放标准， 把 RNA-seq、单细胞、结构生物学、分子动力学、多肽设计与文献挖掘等分析流程， 封装成任何 AI Agent 都能即插即用的技能。
把可复现的科研分析流程，变成 Agent 可以直接调用的技能
git clone https://github.com/ssinder/bioinformatics-agent-skills.git
cp -r bioinformatics-agent-skills/skills/* ~/.claude/skills/
重启宿主后技能即被自动发现。完整说明见 快速上手。
| 特性 | 说明 |
|---|---|
| 开放标准 | SKILL.md + scripts/ + references/，遵循 agentskills.io 规范，兼容 Claude Code、Cursor、Codex 等宿主 |
| 优雅降级 | --help 属于元信息查询，不会因缺少 numpy / pandas 等科学计算栈而崩溃；真正用到该功能时才提示安装 |
| 零重型依赖 | 核心安装仅需 requests + pyyaml，其余按需通过 extras 安装 |
| 跨版本兼容 | CI 覆盖 Python 3.9 / 3.11 / 3.13 |
| 质量保障 | 6 条流水线：规范校验、语法与 lint、单测、依赖与凭据安全扫描、PR 技能扫描、发布 |
| bulk-rnaseq | This skill should be used when running bulk RNA-seq differential expression analysis: FastQC/trimming, Salmon quantification, counts matrix construction, DESeq2 statistics, GO/KEGG enrichment and publication figures. 用于 bulk 转录组（RNA-seq）差异表达分析全流程。 |
| literature-search | This skill should be used when mining academic literature from PubMed, OpenAlex or Semantic Scholar — searching papers by topic or keywords, deduplicating multi-source results, filtering by relevance or citation count, enriching missing abstracts, and exporting RIS, BibTeX or GB/T 7714 citations. 用于多源学术文献检索、去重、相关性筛选、摘要富集与参考文献格式导出的场景。 |
| molecular-dynamics | Analyses molecular-dynamics trajectories with a self-contained pure-numpy DCD and PDB trajectory parser plus built-in Kabsch-Sander alignment, SVD-based PCA, hierarchical clustering of RMSD matrices, geometric hydrogen-bond detection, RMSF, radius of gyration, Ramachandran analysis, inter-chain contacts and Shrake-Rupley SASA. This skill should be used when trajectory RMSD or RMSF, PCA, conformational clustering, hydrogen-bond occupancy, Ramachandran plots or solvent-accessible surface analysis is requested. |
| peptide-design | This skill should be used when analyzing or designing antimicrobial peptides — computing physicochemical properties such as molecular weight, isoelectric point, Kyte-Doolittle hydrophobicity and instability index, classifying peptides as antimicrobial or non-antimicrobial from GO terms and sequence features, deduplicating peptide libraries by clustering, and exporting FASTA or CSV. 用于多肽理化性质计算、抗菌肽判别、序列聚类去冗余与导出的场景。 |
| protein-interactions | Analyzes protein-ligand and protein-protein interactions from PLIP XML reports and AlphaFold model packages using a self-contained standard-library XML parser: extracts residue-level salt bridges, hydrogen bonds, hydrophobic, pi-stacking, water bridges, halogen bonds and metal complexes, ranks hotspot residues, and emits Mermaid network graphs plus PyMOL annotation scripts. This skill should be used when interaction detection, hotspot ranking, PLIP report parsing, interaction network visualisation or AlphaFold confidence analysis is requested. |
| protein-structure | Analyzes protein structures from PDB files: parses ATOM/HETATM records with a dependency-free pure-Python parser, computes radius of gyration, gyration tensor and dipole moments, assigns secondary structure via DSSP or a built-in Kabsch-Sander hydrogen-bond implementation, and optionally retrieves UniProt metadata. This skill should be used when secondary structure assignment, Rg, shape analysis, DSSP, PDB parsing or protein structure annotation is requested. |
| scientific-figures | This skill should be used when generating publication-ready scientific figures — ROC curves, confusion matrix heatmaps, docking binding-energy heatmaps, pLDDT confidence histograms, SHAP summary beeswarms, class distribution charts and other chart types with a unified journal-grade visual style. 用于生成顶刊级出版图表（ROC 曲线、混淆矩阵、热图、pLDDT 分布、SHAP 摘要等）的场景。 |
| single-cell-rnaseq | This skill should be used when running single-cell RNA-seq analysis: reading 10x/AnnData matrices, QC filtering, normalization, HVG selection, PCA, clustering, UMAP/t-SNE and cell type annotation. 用于单细胞转录组（scRNA-seq）质控、降维、聚类与细胞注释全流程。 |
普通脚本仓库要求使用者自己读文档、拼命令、判断参数。
Agent Skills 把这些知识写进了技能描述里 —— Agent 读一眼 SKILL.md
就知道该用哪个技能、怎么调、要注意什么。```yaml
—
name: bulk-rnaseq
description: >
This skill should be used when running bulk RNA-seq differential
expression analysis: FastQC/trimming, Salmon quantification, counts
matrix construction, DESeq2 statistics, GO/KEGG enrichment and
publication figures. 用于 bulk 转录组（RNA-seq）差异表达分析全流程。
—
这段描述就是 Agent 的路由依据。
## 文档
- [快速上手](/bioinformatics-agent-skills/getting-started.html) —— 安装、配置、首次使用
- [技能总览](/bioinformatics-agent-skills/skills/) —— 全部技能及其适用场景
- [技能规范](/bioinformatics-agent-skills/SKILL_SPEC.html) —— 如何编写一个新技能
- [贡献指南](https://github.com/ssinder/bioinformatics-agent-skills/blob/main/CONTRIBUTING.md)
## 引用
如果你在研究中使用了本项目，请引用：
```bibtex
@misc{bioinfoagentskills2026,
title = {BioinfoAgent Skills: An Open Standard Agent Skills Library for Computational Biology},
author = {ssinder},
year = {2026},
howpublished = {\url{https://github.com/ssinder/bioinformatics-agent-skills}},
note = {Accessed: 2026-10-25}
}
MIT，见 LICENSE。