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---
title: "Introduction"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Introduction}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# Introduction
`MicrobiomeR` is a microbiome workflow package that uses [phyloseq](https://github.com/joey711/phyloseq) for
data import, [taxa](https://github.com/ropensci/taxa) for the primary R object called a Taxmap,
[metacoder](https://github.com/grunwaldlab/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](https://grunwaldlab.github.io/metacoder_documentation/) package by providing tools that mimic
some of the functionalities of the [phyloseq](http://joey711.github.io/phyloseq/) package. The key difference is
that the main data object is a [taxa::taxmap object](https://github.com/ropensci/taxa#the-taxmap-class)
instead of a [phyloseq::phyloseq object](http://joey711.github.io/phyloseq/import-data.html#import_biom).
## What makes MicrobiomeR special?
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.
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