Package: MicrobiotaProcess
Type: Package
Title: A comprehensive R package for managing and analyzing microbiome
        and other ecological data within the tidy framework
Version: 1.21.2
Authors@R: c(person("Shuangbin", "Xu", email = "xshuangbin@163.com", role = c("aut", "cre"), comment=c(ORCID="0000-0003-3513-5362")),
             person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-6485-8781")))
Description: MicrobiotaProcess is an R package for analysis, visualization and 
    biomarker discovery of microbial datasets. It introduces MPSE class, this make it
    more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy 
    microbiome data structure paradigm and analysis grammar. It provides a wide variety 
    of microbiome data analysis procedures under the unified and common framework (tidy-like framework).
Depends: R (>= 4.0.0)
Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel,
        vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang,
        tibble, grDevices, stats, utils, coin, ggsignif, patchwork,
        ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>=
        1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table,
        ggfun (>= 0.1.1)
Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn,
        DECIPHER, randomForest, jsonlite, biomformat, scales, yaml,
        withr, S4Vectors, purrr, seqmagick, glue, ggupset,
        ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq,
        aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext,
        DirichletMultinomial, ggpp, BiocManager
License: GPL (>= 3.0)
URL: https://github.com/YuLab-SMU/MicrobiotaProcess/
BugReports: https://github.com/YuLab-SMU/MicrobiotaProcess/issues
VignetteBuilder: knitr
ByteCompile: true
Encoding: UTF-8
biocViews: Visualization, Microbiome, Software, MultipleComparison,
        FeatureExtraction
RoxygenNote: 7.3.2
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: devel
git_last_commit: 0822a21
git_last_commit_date: 2025-09-23
Repository: Bioconductor 3.22
Date/Publication: 2025-09-24
NeedsCompilation: no
Packaged: 2025-09-24 21:00:57 UTC; biocbuild
Author: Shuangbin Xu [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3513-5362>),
  Guangchuang Yu [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>)
Maintainer: Shuangbin Xu <xshuangbin@163.com>
Built: R 4.5.1; ; 2025-09-25 02:47:47 UTC; unix
