In CharlieCarpenter/tidy.micro: A Pipeline For Microbiome Analysis And Visualization

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

tidy.micro

A pipeline for microbiome analysis and visualization

Main Features

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

• Data visualization for exploration

• Calculate, analyze, and visualize diversity measures

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

• Create stacked bar charts based on negative binomial model estiamtes

• Longitudinal and Three Mode PCA plots

Intallation

# install.packages("devtools")
devtools::install_github("CharlieCarpenter/tidy.micro")

Vignette

For a comprehensive walk through please see our vignette.

CharlieCarpenter/tidy.micro documentation built on Jan. 19, 2020, 6:28 p.m.