Package: ADAPT Title: Analysis of Microbiome Differential Abundance by Pooling Tobit Models Version: 1.7.0 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: https://bioc.r-universe.dev Date/Publication: 2026-04-28 13:03:42 UTC RemoteUrl: https://github.com/bioc/ADAPT RemoteRef: HEAD RemoteSha: c76579fcac1ac5d28fe5983aae773673be1769a5 NeedsCompilation: yes Packaged: 2026-06-19 06:53:01 UTC; root Author: Mukai Wang [aut, cre] (ORCID: ), Simon Fontaine [ctb], Hui Jiang [ctb], Gen Li [aut, ctb] Maintainer: Mukai Wang