ADAPT
This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see ADAPT.
Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Bioconductor version: 3.21
ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones.
Author: Mukai Wang [aut, cre] ORCID iD ORCID: 0000-0002-1413-1904 , Simon Fontaine [ctb], Hui Jiang [ctb], Gen Li [aut, ctb]
Maintainer: Mukai Wang <wangmk at umich.edu>
citation("ADAPT")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ADAPT")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ADAPT")
Details
Package Archives
Follow Installation instructions to use this package in your R session.