curatedMetagenomicData
This is the released version of curatedMetagenomicData; for the devel version, see curatedMetagenomicData.
All Bioconductor versions of curatedMetagenomicData
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4
Curated Metagenomic Data of the Human Microbiome
Bioconductor version: 3.23 · Package version: 3.20.0
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.
Author: Lucas schiffer [aut, cre] 
, 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], Sehyun Oh [ctb], Yoon-Ji Jung [ctb]
Maintainer: Lucas schiffer <schiffer.lucas at gmail.com>
Citation
From within R, enter citation("curatedMetagenomicData"):
Lucas schiffer, Levi Waldron. curatedMetagenomicData: Curated Metagenomic Data of the Human Microbiome. doi:10.18129/B9.bioc.curatedMetagenomicData, R package version 3.20.0, https://bioconductor.org/packages/curatedMetagenomicData.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("curatedMetagenomicData")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 3.20.0 |
| License | Artistic-2.0 |
| URL | https://github.com/waldronlab/curatedMetagenomicData |
| Bug Reports | https://github.com/waldronlab/curatedMetagenomicData/issues |
| Last updated | 2026-05-05 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 years) |
| Downloads rank | 23 of 434 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch |
| Package Short Url | https://bioconductor.org/packages/curatedMetagenomicData/ |
Documentation
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | curatedMetagenomicData_3.20.0.tar.gz |
| Source Repository | git clone https://git.bioconductor.org/packages/curatedMetagenomicData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/curatedMetagenomicData |
| Package Downloads Report | Download Stats |
Dependencies
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
Reverse dependencies
Suggests Me (4): CrcBiomeScreen, lefser, MMUPHin, OmicsMLRepoR