Package: benchdamic
Type: Package
Title: Benchmark of differential abundance methods on microbiome data
Version: 1.16.0
Authors@R: 
    c(person(given = "Matteo", 
             family = "Calgaro", 
             email = "mcalgaro93@gmail.com",
             role = c("aut", "cre"),
             comment = c(ORCID = "0000-0002-3056-518X")),
      person(given = "Chiara", 
             family = "Romualdi", 
             role = c("aut"),
             comment = c(ORCID = "0000-0003-4792-9047")),
      person(given = "Davide", 
             family = "Risso", 
             email = "mcalgaro93@gmail.com",
             role = c("aut"),
             comment = c(ORCID = "0000-0001-8508-5012")),
      person(given = "Nicola", 
             family = "Vitulo", 
             role = c("aut"),
             comment = c(ORCID = "0000-0002-9571-0747")))       
Description: Starting from a microbiome dataset (16S or WMS with
        absolute count values) it is possible to perform several
        analysis to assess the performances of many differential
        abundance detection methods. A basic and standardized version
        of the main differential abundance analysis methods is supplied
        but the user can also add his method to the benchmark. The
        analyses focus on 4 main aspects: i) the goodness of fit of
        each method's distributional assumptions on the observed count
        data, ii) the ability to control the false discovery rate, iii)
        the within and between method concordances, iv) the
        truthfulness of the findings if any apriori knowledge is given.
        Several graphical functions are available for result
        visualization.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.3.0)
Imports: stats, stats4, utils, methods, phyloseq,
        TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR,
        DESeq2, limma, ALDEx2, corncob, SummarizedExperiment, MAST,
        Seurat, ANCOMBC, microbiome, mixOmics, lme4, NOISeq, dearseq,
        MicrobiomeStat, Maaslin2, maaslin3, GUniFrac, metagenomeSeq,
        MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro,
        ggridges, graphics, cowplot, grDevices, tidytext
Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq,
        testthat
VignetteBuilder: knitr
LazyData: TRUE
RoxygenNote: 7.3.3
biocViews: Metagenomics, Microbiome, DifferentialExpression,
        MultipleComparison, Normalization, Preprocessing, Software
BugReports: https://github.com/mcalgaro93/benchdamic/issues
Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev
        libgmp3-dev make libgsl0-dev texlive libicu-dev libjpeg-dev
        libpng-dev libxml2-dev libmpfr-dev libgl1-mesa-dev libssl-dev
        python3 libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:13:16 UTC
RemoteUrl: https://github.com/bioc/benchdamic
RemoteRef: RELEASE_3_22
RemoteSha: fcdab2ab44a609f05aa576cbbff58d10fb75e234
NeedsCompilation: no
Packaged: 2025-11-24 16:35:23 UTC; root
Author: Matteo Calgaro [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3056-518X>),
  Chiara Romualdi [aut] (ORCID: <https://orcid.org/0000-0003-4792-9047>),
  Davide Risso [aut] (ORCID: <https://orcid.org/0000-0001-8508-5012>),
  Nicola Vitulo [aut] (ORCID: <https://orcid.org/0000-0002-9571-0747>)
Maintainer: Matteo Calgaro <mcalgaro93@gmail.com>
Built: R 4.5.2; ; 2025-11-24 16:38:51 UTC; windows
