scikit-bio (Claude Skill)

Claude skill wrapping the scikit-bio library for community ecology and microbiome analysis — diversity metrics, ordination, statistical tests, and phylogenetics.

Type	Claude Skill
Supplier	K-Dense Inc. (wraps the BSD-3 scikit-bio library)
Availability	GA
Pricing	Free / OSS (BSD-3-Clause)
Capabilities	Read/Write — local computation on user-supplied sequence and community data

How to install

• Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/genomics-bioinformatics/scikit-bio into ~/.claude/skills/). Install via the Skills CLI (recommended): npx skills add K-Dense-AI/scientific-agent-skills, then enable the scikit-bio skill. Or clone the repo manually:

git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/scikit-bio ~/.claude/skills/
uv pip install scikit-bio

What it does

Recipes covering:

• BIOM, FASTA, FASTQ, and GenBank I/O
• Alpha diversity: Shannon, Simpson, Faith’s PD
• Beta diversity: Bray-Curtis, Jaccard, weighted / unweighted UniFrac
• Ordination: PCoA, RDA, CCA
• Statistics: PERMANOVA, ANOSIM, Mantel
• Phylogenetics: neighbor-joining, UPGMA

Primary use cases: 16S and shotgun microbiome diversity workflows, QIIME 2-style OTU/ASV analyses, community-ecology statistics.

Notes

Pure-Python, runs locally; no auth or external services. Pairs cleanly with QIIME 2 outputs via BIOM.

Sources

• skills/scikit-bio/SKILL.md
• K-Dense-AI/scientific-agent-skills

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