This is the development version of ADAPT; for the stable release version, see ADAPT.
Analysis of Microbiome Differential Abundance by Pooling Tobit ModelsBioconductor version: Development (3.22)
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: 0000-0002-1413-1904 , Simon Fontaine [ctb], Hui Jiang [ctb], Gen Li [aut, ctb]
Maintainer: Mukai Wang <wangmk at umich.edu>
Citation (from within R, entercitation("ADAPT")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ADAPT")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ADAPT")Follow Installation instructions to use this package in your R session.
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