bioMate-AI/biomate-bioconductor-kb

Registry 信息

项目简介

BioMate-KB Bioconductor技能以Claude/Agent技能形式呈现前100个Bioconductor包，基于官方Vignette文档，确保生物信息学工作流程的准确性和可重复性。

要点

• 前100个Bioconductor包作为即用型Claude Skill
• 基于Vignette文档的知识，确保生物信息学分析可靠
• 与Claude及Agent工作流无缝集成
• 可重复且可引用的技能定义

使用场景

• 使用DESeq2自动化RNA-seq差异表达分析
• 通过ChIPseeker进行ChIP-seq峰识别与注释
• 利用clusterProfiler简化基因集富集分析
• 使用mixOmics技能整合多组学数据

README 摘要

# BioMate-KB — Bioconductor Skills [](https://doi.org/10.5281/zenodo.20616355) [](https://doi.org/10.5281/zenodo.20616543) > A knowledge base of 15,641 real-execution-validated Bioconductor workflow steps — the public skill bundle behind [BioMate AI](https://www.biomate.ai). Methodology and validation documented in two preprints (see [Citation](#citation)). **Top 100 Bioconductor packages by official download score, formatted as Claude Code Skills.** A skill bundle in [Claude Code Skills](https://docs.anthropic.com/en/docs/claude-code/skills-overview) format, covering the most-used 100 Bioconductor packages from the BioMate-KB knowledge base. Each skill teaches Claude when to choose a package, what parameters to set, how to interpret results, and what pitfalls to avoid. ## What's here ``` skills/ ├── transcriptomics/ (33 skills — DESeq2, edgeR, limma, fgsea, ...) ├── genomics/ (23 skills — GenomicRanges, Rsamtools, ...) ├── general/ (16 skills — utility / cross-domain) ├── proteomics/ (8 skills — MSstats, MSnbase, Spectra, ...) ├── variant-calling/ (4 skills — VariantAnnotation, maftools, ...) ├── metagenomics/ (4 skills — phyloseq, ANCOMBC, dada2, ...) ├── single-cell/ (3 skills — Seurat, scran, scater, ...) ├── epigenomics/ (3 skills — ChIPseeker, DiffBind, methylKit, ...) ├── enrichment/ (2 skills — clusterProfiler, ReactomePA, ...) ├── annotation/ (2 skills — biomaRt, AnnotationHub, ...) └── imaging/ (2 skills) ``` This bundle is intentionally focused on the **highest-traffic packages** — the top 100 accounts for roughly 60% of all Bioconductor

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