Claude Skill
bioMate-AI/biomate-bioconductor-kb
BioMate-KB Bioconductor Skills offers the top 100 Bioconductor packages as Claude/agent skills, grounded in official vignettes for accurate, reproducible bioinformatics workflows.
Overview
Repository
Install this Skill
git clone https://github.com/bioMate-AI/biomate-bioconductor-kb.gitRegistry
Summary
BioMate-KB Bioconductor Skills provides the top 100 Bioconductor packages as Claude/agent skills, grounded in official vignettes for accurate, reproducible bioinformatics workflows.
BioMate-KB Bioconductor技能——以Claude/Agent技能形式呈现的Top 100包，基于Vignette文档
Key features
- Top 100 Bioconductor packages as ready-to-use Claude skills
- Vignette-grounded knowledge for reliable bioinformatics analysis
- Seamless integration with Claude and agent workflows
- Reproducible and citation-ready skill definitions
Use cases
- Automate RNA-seq differential expression analysis with DESeq2
- Perform ChIP-seq peak calling and annotation via ChIPseeker
- Streamline gene set enrichment analysis using clusterProfiler
- Integrate multi-omics data with mixOmics skills
README excerpt
# 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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