In CharlieCarpenter/tidyMicro: A Pipeline for Microbiome Analysis and Visualization

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

tidyMicro

The goal of tidyMicro is to provide a cohesive pipeline for microbiome data analysis and visualization.

Installation

You can install the latest version of tidyMicro from this GitHub using

devtools::install_github("CharlieCarpenter/tidyMicro", 
                         build_vignettes = TRUE) ## Recommended

Or you can install the latest release of tidyMicro from CRAN using

install.packages("tidyMicro")

Main Features

• Merge any number OTU tables with clinical data into one tidy data set

• Data visualization for exploration

• Calculate, analyze, and visualize diversity measures

• Fit negative binomial, beta binomial, rank sum, and presence absence models

• Create stacked bar charts based on negative binomial and beta binomial model estimates

• Longitudinal PCA plots

CharlieCarpenter/tidyMicro documentation built on April 25, 2021, 4:09 p.m.