ADAPT

Installation

There are two ways of installing the package. One is through the GitHub repository and the other is through the Bioconductor repository.

# install Bioconductor first
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# the first way is to install from GitHub
if (!require("ADAPT"))
    BiocManager::install("mkbwang/ADAPT", build_vignettes = TRUE)

# the second way is install from Bioconductor repository
if (!require("ADAPT"))
    BiocManager::install("ADAPT", version="devel", build_vignettes = TRUE)

The installation may take around five minutes.

The authors are preparing to submit this package to bioconductor.

Introduction

ADAPT stands for "Analysis of microbiome differential abundance by pooling Tobit models". There are two main innovations:

• ADAPT treats zero counts as left censored observations and use Tobit models to model the log count ratios.
• ADAPT has an innovative way of selecting non-differentially abundant taxa as reference taxa. It then uses the reference taxa to find the differentially abundant ones.

To learn more about the usage of ADAPT, type in R console

library(ADAPT)
browseVignettes(package="ADAPT")

The codes of simulation studies and real data analyses in the manuscript are in this GitHub repository.