Package: ADAPT Title: Analysis of Microbiome Differential Abundance by Pooling Tobit Models Version: 1.6.0 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: libglpk-dev make libicu-dev libxml2-dev zlib1g-dev Repository: Bioconductor 3.23 Date/Publication: 2026-04-28 13:03:42 UTC RemoteUrl: https://github.com/bioc/ADAPT RemoteRef: RELEASE_3_23 RemoteSha: 6e0cbf87732a87d24e7f9e33a74f52b07570b315 NeedsCompilation: yes Packaged: 2026-07-07 10:29:11 UTC; root Author: Mukai Wang [aut, cre] (ORCID: ), Simon Fontaine [ctb], Hui Jiang [ctb], Gen Li [aut, ctb] Maintainer: Mukai Wang