mia - Microbiome analysis

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

Contribution

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

Technical aspects

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/)

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")

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.