DESCRIPTION

Package: curatedMetagenomicData
Title: Curated Metagenomic Data of the Human Microbiome
Description:
    The curatedMetagenomicData package provides standardized, curated human
    microbiome data for novel analyses. It includes gene families, marker
    abundance, marker presence, pathway abundance, pathway coverage, and
    relative abundance for samples collected from different body sites. The
    bacterial, fungal, and archaeal taxonomic abundances for each sample were
    calculated with MetaPhlAn3, and metabolic functional potential was
    calculated with HUMAnN3. The manually curated sample metadata and
    standardized metagenomic data are available as (Tree)SummarizedExperiment
    objects.
Authors@R:
    c(person(given = "Lucas", family = "schiffer", role = c("aut", "cre"),
             email = "schiffer.lucas@gmail.com",
             comment = c(ORCID = "0000-0003-3628-0326")),
      person(given = "Levi", family = "Waldron", role = "aut"),
      person(given = "Edoardo", family = "Pasolli", role = "ctb"),
      person(given = "Jennifer", family = "Wokaty", role = "ctb"),
      person(given = "Sean", family = "Davis", role = "ctb"),
      person(given = "Audrey", family = "Renson", role = "ctb"),
      person(given = "Chloe", family = "Mirzayi", role = "ctb"),
      person(given = "Paolo", family = "Manghi", role = "ctb"),
      person(given = "Samuel", family = "Gamboa-Tuz", role = "ctb"),
      person(given = "Marcel", family = "Ramos", role = "ctb"),
      person(given = "Valerie", family = "Obenchain", role = "ctb"),
      person(given = "Kelly", family = "Eckenrode", role = "ctb"),
      person(given = "Nicola", family = "Segata", role = "ctb"))
biocViews:
    ExperimentHub,
    Homo_sapiens_Data,
    MicrobiomeData,
    ReproducibleResearch
Version: 3.15.0
License: Artistic-2.0
Depends:
    R (>= 4.1.0),
    SummarizedExperiment,
    TreeSummarizedExperiment
Imports:
    AnnotationHub,
    ExperimentHub,
    S4Vectors,
    dplyr,
    magrittr,
    mia,
    purrr,
    rlang,
    stringr,
    tibble,
    tidyr,
    tidyselect
Suggests:
    BiocStyle,
    DT,
    knitr,
    readr,
    rmarkdown,
    scater,
    testthat,
    utils,
    uwot,
    vegan
URL: https://github.com/waldronlab/curatedMetagenomicData
BugReports: https://github.com/waldronlab/curatedMetagenomicData/issues
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
VignetteBuilder: knitr