MicrobiomeR is a microbiome workflow package that uses phyloseq for data import, taxa for the primary R object called a Taxmap, metacoder for data analysis, and a combination of packages for data visualization including ggplot2.
The goal of this package is to enhance the use of the metacoder package by providing tools that mimic some of the functionalities of the phyloseq package. The key difference is that the main data object is a taxa::taxmap object instead of a phyloseq::phyloseq object.
MicrobiomeR boasts a seamless and comprehensive workflow to analyze microbiome data which (1) emphasizes statistical rigor, (2) simplifies the creation of beautiful, meaningful, and easily reproducible publication-ready visualizations, and (3) adds versatile functions that incorporates the most widely used microbiome packages for R including vegan, microbiome, taxa, phyloseq, and metacoder.