Package: ADAPT
Title: Analysis of Microbiome Differential Abundance by Pooling Tobit
        Models
Version: 1.6.1
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: Bioconductor 3.23
Date/Publication: 2026-10-16 15:18:54 UTC
RemoteUrl: https://github.com/bioc/ADAPT
RemoteRef: RELEASE_3_23
RemoteSha: 3d23885f10737af86cab883ee34664cd9c2cbdc0
NeedsCompilation: yes
Packaged: 2026-10-16 17:44:00 UTC; root
Author: Mukai Wang [aut, cre] (ORCID: <https://orcid.org/0000-0002-1413-1904>),
  Simon Fontaine [ctb],
  Hui Jiang [ctb],
  Gen Li [aut, ctb]
Maintainer: Mukai Wang <wangmk@umich.edu>
Built: R 4.6.1; aarch64-apple-darwin23; 2026-10-16 17:59:18 UTC; unix
