Package: ADAPT
Title: Analysis of Microbiome Differential Abundance by Pooling Tobit
        Models
Version: 1.4.0
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 libssl-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:32:05 UTC
RemoteUrl: https://github.com/bioc/ADAPT
RemoteRef: RELEASE_3_22
RemoteSha: f9fd0d96b97e9d819eea9de80832cf07eb4d5e51
NeedsCompilation: yes
Packaged: 2026-02-02 09:57:16 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 4.5.2; x86_64-w64-mingw32; 2026-02-02 09:59:08 UTC; windows
Archs: x64
