# Bioconductor Phyloseq

Phyloseq provides a set of classes and tools to facilitate the import, storage...

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-phyloseq -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-phyloseq -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-phyloseq -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-phyloseq -g -a gemini-cli -y`

## Description

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# phyloseq

## Dependencies & Environment

> Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

- **Version:** 1.56.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6
- **Imports:** ade4, ape, Biobase, BiocGenerics, biomformat, Biostrings, cluster, data.table, foreach, ggplot2, igraph, multtest, plyr, reshape2, scales, vegan
- **Install:** `BiocManager::install("phyloseq")`

## When to Use
- Importing and storing complex phylogenetic sequencing data (OTU tables, sample metadata, taxonomy, trees) into a single object using `import()`.
- Estimating and visualizing alpha diversity using `plot_richness()` with measures like "Chao1" or "Shannon".
- Performing beta diversity ordination (e.g., PCoA, NMDS, CCA) using `ordinate()` and visualizing the results with `plot_ordination()`.
- Creating exploratory bar plots of taxonomic abundance across samples using `plot_bar()`.

## When NOT to Use
- For advanced network analysis beyond basic ecological similarity, use `igraph` directly because `plot_net()` provides only a default Jaccard co-occurrence network.
- For complex custom plotting beyond standard wrappers, use `ggplot2` directly because `phyloseq` wrappers are built on it but may restrict advanced geoms.

## Data Requirements
- Pre-clustered phylogenetic sequencing data (OTU/ASV table).
- Associated sample data (metadata), a phylogenetic tree, and/or taxonomic assignments.
- Raw (untrimmed) OTU-clustered data is strictly required when performing richness estimates.

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/metagenomics/phyloseq/SKILL.md