Package: ADAPT Title: Analysis of Microbiome Differential Abundance by Pooling Tobit Models Version: 1.7.1 Authors@R: c(person(given="Mukai", family="Wang", email="wangmk@umich.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1413-1904")), person(given="Simon", family="Fontaine", email="simfont@umich.edu", role = "ctb"), person(given="Hui", family="Jiang", email="jianghui@umich.edu", role="ctb"), person(given="Gen", family="Li", email="ligen@umich.edu", role=c("aut", "ctb"))) Description: 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. License: MIT + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.2 Imports: Rcpp (>= 1.0.8), RcppArmadillo (>= 0.10.8), RcppParallel (>= 5.1.5), phyloseq (>= 1.39.0), methods, stats, ggplot2 (>= 3.4.1), ggrepel (>= 0.9.1) Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0) Config/testthat/edition: 3 LinkingTo: Rcpp, RcppArmadillo, RcppParallel biocViews: DifferentialExpression, Microbiome, Normalization, Sequencing, Metagenomics, Software, MultipleComparison Depends: R (>= 4.1.0) LazyData: false VignetteBuilder: knitr Config/pak/sysreqs: cmake libglpk-dev libicu-dev libxml2-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-10-16 15:21:35 UTC RemoteUrl: https://github.com/bioc/ADAPT RemoteRef: HEAD RemoteSha: 85b835f558a1d769b8bc7204c356042367e7a165 NeedsCompilation: yes Packaged: 2026-10-16 17:40:13 UTC; root Author: Mukai Wang [aut, cre] (ORCID: ), Simon Fontaine [ctb], Hui Jiang [ctb], Gen Li [aut, ctb] Maintainer: Mukai Wang