Package: benchdamic
Type: Package
Title: Benchmark of differential abundance methods on microbiome data
Version: 1.14.0
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, 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: 7.3.2
biocViews: Metagenomics, Microbiome, DifferentialExpression,
        MultipleComparison, Normalization, Preprocessing, Software
BugReports: https://github.com/mcalgaro93/benchdamic/issues
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_21
git_last_commit: f19585c
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-15 23:38:34 UTC; biocbuild
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 4.5.0; ; 2025-04-16 13:57:12 UTC; windows
