Package: curatedMetagenomicData
Title: Curated Metagenomic Data of the Human Microbiome
Version: 3.21.1
Date: 2025-9-26
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("Lucas", "schiffer", , "schiffer.lucas@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-3628-0326")),
    person("Levi", "Waldron", role = "aut"),
    person("Edoardo", "Pasolli", role = "ctb"),
    person("Jennifer", "Wokaty", role = "ctb"),
    person("Sean", "Davis", role = "ctb"),
    person("Audrey", "Renson", role = "ctb"),
    person("Chloe", "Mirzayi", role = "ctb"),
    person("Paolo", "Manghi", role = "ctb"),
    person("Samuel", "Gamboa-Tuz", role = "ctb"),
    person("Marcel", "Ramos", role = "ctb"),
    person("Valerie", "Obenchain", role = "ctb"),
    person("Kelly", "Eckenrode", role = "ctb"),
    person("Nicola", "Segata", role = "ctb"),
    person("Tuomas", "Borman", role = "ctb",
           comment = c(ORCID = "0000-0002-8563-8884")),
    person("Sehyun", "Oh", role = "ctb"),
    person("Yoon-Ji", "Jung", role = "ctb"),
    person("NCI", role = "fnd",
           comment = c(GrantNo. = "R01CA230551"))
  )
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, OmicsMLRepoR, lefser
URL: https://github.com/waldronlab/curatedMetagenomicData
BugReports: https://github.com/waldronlab/curatedMetagenomicData/issues
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: ExperimentHub, Homo_sapiens_Data, MicrobiomeData,
        ReproducibleResearch
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make libgsl0-dev
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libuv1-dev libwebp-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://waldronlab.r-universe.dev
Date/Publication: 2026-05-14 20:39:48 UTC
RemoteUrl: https://github.com/waldronlab/curatedMetagenomicData
RemoteRef: HEAD
RemoteSha: cecdfeca42d0f6cda6bad3f5c755c5c4ba4da858
NeedsCompilation: no
Packaged: 2026-06-15 07:30:25 UTC; root
Author: Lucas schiffer [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3628-0326>),
  Levi Waldron [aut],
  Edoardo Pasolli [ctb],
  Jennifer Wokaty [ctb],
  Sean Davis [ctb],
  Audrey Renson [ctb],
  Chloe Mirzayi [ctb],
  Paolo Manghi [ctb],
  Samuel Gamboa-Tuz [ctb],
  Marcel Ramos [ctb],
  Valerie Obenchain [ctb],
  Kelly Eckenrode [ctb],
  Nicola Segata [ctb],
  Tuomas Borman [ctb] (ORCID: <https://orcid.org/0000-0002-8563-8884>),
  Sehyun Oh [ctb],
  Yoon-Ji Jung [ctb],
  NCI [fnd] (GrantNo.: R01CA230551)
Maintainer: Lucas schiffer <schiffer.lucas@gmail.com>