Differential Abundance (bioSkills)

A Claude Code skill that tests which individual taxa differ between groups in an amplicon feature table, using compositionally-aware methods and reporting the consensus across several of them rather than one tool’s hit list.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT) — phyloseq, ALDEx2, ANCOMBC, MaAsLin, LinDA, ZicoSeq, LEfSe and QIIME2 are separately installed OSS
Capabilities Read/Write — Claude runs the skill’s workflow locally (R), not as an MCP tool
Verified works · 2026-08-03
Security cleared · 2026-08-03 — GPTomics/bioSkills MIT confirmed, provenance matches, no advisories

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

  • Claude Code — clone and install via the bundled script: 
    git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "microbiome"

    The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview the skills first.

  • Claude Code / other agents — copy just this one skill: 
    cp -r bioSkills/microbiome/differential-abundance ~/.claude/skills/

    (run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). Install the R packages for the chosen methods when prompted on first use.

What it does

Runs several differential-abundance methods on one feature table and reconciles them:

  • Workflow — load a phyloseq object and apply a prevalence filter (10–25% of samples) to drop rare features and stabilize multiple-testing correction; run at least two methods from the panel on the same table; intersect the significant-taxa sets, reporting the intersection as high-confidence and the union as exploratory with per-taxon tool agreement; gate results on an effect-size floor alongside BH/FDR.
  • Method panel — ALDEx2 (Dirichlet Monte-Carlo CLR, conservative), ANCOM-BC2/ANCOMBC (sampling-fraction bias correction, structural zeros, passed_ss, Holm default), MaAsLin2/MaAsLin3 (multivariable GLM with random effects and a prevalence/abundance split), LinDA (CLR mixed-model regression), ZicoSeq (permutation FDR), LEfSe, and QIIME2 q2-composition ancombc.
  • Interpretation guidance — the Nearing benchmark finding that the hit list depends more on the chosen tool than on the biology (hence the consensus deliverable); why a relative change is not an absolute one without a microbial-load anchor; the prevalence-filter knob; and why DESeq2/edgeR misfire on compositional amplicon data.

Primary use cases: taxa differing between case and control groups, covariate-adjusted or longitudinal microbiome designs, choosing a differential-abundance method.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally rather than as an MCP server. The upstream skill front-matter name is bio-microbiome-differential-abundance; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /differential-abundance. Consumes the ASV table built by Amplicon Processing and labelled by Taxonomy Assignment. The skill routes whole-community questions to the microbiome diversity-analysis skill and shotgun differential abundance to the metagenomics category instead of answering them here. Upstream directory: microbiome/differential-abundance.

Sources

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