# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "curatedMetagenomicData" in publications use:'
type: software
license: Artistic-2.0
title: 'curatedMetagenomicData: Curated Metagenomic Data of the Human Microbiome'
version: 3.21.1
doi: 10.1038/nmeth.4468
identifiers:
- type: doi
  value: 10.32614/CRAN.package.curatedMetagenomicData
abstract: 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:
- family-names: schiffer
  given-names: Lucas
  email: schiffer.lucas@gmail.com
  orcid: https://orcid.org/0000-0003-3628-0326
- family-names: Waldron
  given-names: Levi
preferred-citation:
  type: article
  title: Accessible, curated metagenomic data through ExperimentHub
  authors:
  - family-names: Pasolli
    given-names: Edoardo
  - family-names: Schiffer
    given-names: Lucas
    email: schiffer.lucas@gmail.com
    orcid: https://orcid.org/0000-0003-3628-0326
  - family-names: Manghi
    given-names: Paolo
  - family-names: Renson
    given-names: Audrey
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Truong
    given-names: Duy Tin
  - family-names: Beghini
    given-names: Francesco
  - family-names: Malik
    given-names: Faizan
  - family-names: Ramos
    given-names: Marcel
  - family-names: Dowd
    given-names: Jennifer B
  - family-names: Huttenhower
    given-names: Curtis
  - family-names: Morgan
    given-names: Martin
  - family-names: Segata
    given-names: Nicola
  - family-names: Waldron
    given-names: Levi
  journal: Nat. Methods
  volume: '14'
  issue: '11'
  month: '10'
  year: '2017'
  issn: 1548-7091, 1548-7105
  doi: 10.1038/nmeth.4468
  start: '1023'
  end: '1024'
repository: https://waldronlab.r-universe.dev
repository-code: https://github.com/waldronlab/curatedMetagenomicData
commit: cecdfeca42d0f6cda6bad3f5c755c5c4ba4da858
url: https://github.com/waldronlab/curatedMetagenomicData
date-released: '2025-09-26'
contact:
- family-names: schiffer
  given-names: Lucas
  email: schiffer.lucas@gmail.com
  orcid: https://orcid.org/0000-0003-3628-0326