biomate-bioconductor-kb
BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes
BioMate-KB Bioconductor Skills is a collection of 200 agent skills designed for Claude Code, covering the top 100 most-downloaded Bioconductor packages plus 100 fast-growing analysis packages. Each skill provides vignette-grounded instructions on when to choose a package, workflow recipes for distinct analyses, parameter guidance, result interpretation tips, and common pitfalls. The skills span 12 bioinformatics domains including transcriptomics, genomics, proteomics, single-cell analysis, and metagenomics, with 390 workflow recipes across the 200 packages. All skill content is fact-verified against official Bioconductor vignettes and pinned to Bioconductor 3.21 for reproducibility.
Key Features
Use Cases
- 01Enabling AI agents to select and configure DESeq2, edgeR, or limma for bulk RNA-seq differential expression analysis
- 02Guiding workflow routing from natural-language bioinformatics requests to appropriate Bioconductor packages and parameters
- 03Teaching Claude Code how to interpret ChIP-seq, methylation, or epigenomic analysis results with domain-specific context
- 04Providing AI assistants with step-by-step recipes for single-cell, spatial transcriptomics, and proteomics workflows
- 05Surfacing newly-important analysis methods through rising-star package skills before they reach top download rankings
- 06Offering AI agents parameter recommendations, pitfalls, and alternatives for 200 Bioconductor analysis packages
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biomate-bioconductor-kb — FAQ
What is BioMate-KB Bioconductor Skills?+
It is a collection of 200 Claude Code Skills in SKILL.md format that teach AI agents when and how to use Bioconductor R packages for bioinformatics analysis. Each skill is grounded in official package vignettes and includes workflow recipes, parameter guidance, and common pitfalls.
How do I install these skills in Claude Code?+
Clone the repository, then copy SKILL.md files from the skills/ directory into ~/.claude/skills/ (global) or .claude/skills/ (project-level). Claude Code automatically discovers skills in those directories. You can install all 200 or filter by domain (e.g., only transcriptomics skills).
Which AI clients support these Bioconductor skills?+
These skills are formatted for Claude Code (Anthropic's AI coding assistant). The SKILL.md format follows Claude Code's skills specification and requires Claude Code to function.
Do I need API keys or Bioconductor installed to use these skills?+
The skills themselves are knowledge files that require no API keys. However, to execute the workflows they describe, you need either a local R/Bioconductor installation or access to BioMate Cloud, which is free for academic and non-profit researchers.
Is BioMate-KB Bioconductor Skills free to use?+
Yes, the skill content is released under CC-BY-4.0 and the extraction scripts under Apache-2.0, both permissive open-source licenses. The skills are free to use, share, and adapt with attribution.
What Bioconductor version do these skills cover?+
The skills are pinned to Bioconductor 3.21 with version metadata recorded in MANIFEST.json. This ensures reproducible behavior as Bioconductor releases advance and package APIs change.
How do I install biomate-bioconductor-kb?+
Open the source repository on GitHub and follow its README. biomate-bioconductor-kb is a skill — MCP Agents Market links you directly to the official repo.
Is biomate-bioconductor-kb free?+
biomate-bioconductor-kb is an open-source project hosted on GitHub. Check the repository for its license and any usage requirements.