DESCRIPTION

Package: MicrobiotaProcess
Type: Package
Title: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework 
Version: 1.19.0
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,
  gghalves,
  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: 7.3.1