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.

Currently following things are implemented:

• data wrangling functions (agglomerate*, merge*, and more)
• CCA analysis via vegan package
• Bray-Curtis dissimilarity via vegan package
• JSD and UniFrac distance calculation ported from phyloseq to work with TreeSummarizedExperiment objects
• MDS via the scater package for any other distance objects
• import functions for biom data, DADA2 objects, phyloseq objects and more

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

Let's use a git flow kind of approach. Development version should be done against the master branch and then merged to release for release. (https://guides.github.com/introduction/flow/)

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

BiocManager::install("mia")

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

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

BiocManager::install("mia")

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.