AI agent skill · by @bioMate-AI

Bioconductor Microbiome

Utilities for microbiome analysis.

Archived 2026-10-23 · Source updated 2026-06-20. Check the original repository for the latest version.

SKILL.md instructions

# microbiome

## Dependencies & Environment

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

- **Version:** 1.34.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6
- **Depends:** phyloseq, ggplot2
- **Imports:** Biostrings, compositions, dplyr, reshape2, Rtsne, scales, tibble, tidyr, vegan
- **Install:** `BiocManager::install("microbiome")`

## When to Use
- Facilitating `phyloseq`-based exploration and analysis of taxonomic profiling data.
- Performing manipulation, statistical analysis, and visualization of taxonomic profiling data.
- Standardizing analyses and developing best practices for targeted microbiome analysis.

## When NOT to Use
- For new projects or multi-omics data analysis, use the `miaverse` project instead, as `microbiome` development has been discontinued.
- For workflows based on the new `TreeSummarizedExperiment` data container, use `miaverse` packages instead of `microbiome`.

## Data Requirements
- Taxonomic profiling data in the independent `phyloseq` data format.

## Key Parameters
- No parameters are explicitly detailed in the provided vignette text.

## Best Practices
- Transition to the `miaverse` project and `TreeSummarizedExperiment` data container for added capabilities in multi-omics data analysis.
- Use the package to facilitate scalable exploration of population cohorts and targeted case-control studies.
- Rely on the independent `phyloseq` package and data structures for R-based microbiome analysis.

## Common Pitfalls
- **Using discontinued software for new multi-omics projects**: The `microbiome` package development is discontinued. Fix: Shift to `miaverse` tools based on `TreeSummarizedExperiment`.
- **Incompatibility with new data containers**: Attempting to use `TreeSummarizedExperiment` objects directly in `microbiome`. Fix: Use `phyloseq` format or migrate to `miaverse`.
- **Missing general-purpose tools**: Relying solely on `microbiome` for all analyses. Fix: Integrate with the independent `phyloseq` package and its data structures.

## Alternatives
- **phyloseq**: The independent package and data structure for R-based microbiome analysis that `microbiome` relies heavily upon.
- **miaverse**: The recommended successor project based on the `TreeSummarizedExperiment` data container.

## Citations
- Leo Lahti et al. (Bioconductor, 2017-2020). Tools for microbiome analysis in R. Microbiome package version.

## References
- Homepage: https://bioconductor.org/packages/microbiome
- Vignette: https://bioconductor.org/packages/release/bioc/vignettes/microbiome

<!-- biomate-cta -->
---

## Run this on BioMate

This skill is the **knowledge layer** — when, why, and how to use `microbiome`. To **run this analysis on your own data** with managed compute, automated QC, and reproducible outputs, use **[BioMate](https://www.biomate.ai?ref=kb&pkg=microbiome)** — free to start.

▶ **[Open `microbiome` on BioMate →](https://www.biomate.ai?ref=kb&pkg=microbiome)**