mia - Microbiome analysis

Using the package

This project provides functions and workflows examples for analyses of microbiome data. The main class for working with microbiome data in this package is TreeSummarizedExperiment.

For examples of functionality, see the function reference page.

More information and example workflows are provided in the online manual Orchestrating Microbiome Analysis with Bioconductor.

Note: The rCLR and rAitchison methods require the vegan R package version 2.7-1 (released on 2025-06-06) or later.

Installation

Bioc-release

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mia")

Bioc-devel

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mia")

Contributing

Contributions are welcome in the form of feedback, issues, pull requests etc, see contributor guidelines.

Code of conduct

Please note that the mia project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.