curatedMetagenomicData

This is the released version of curatedMetagenomicData; for the devel version, see curatedMetagenomicData.

All versions

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: Release (3.23)

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] ORCID: 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], 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("curatedMetagenomicData")

curatedMetagenomicData	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch
Version	3.20.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment
Imports	AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia, purrr, rlang, stringr, tibble, tidyr, tidyselect
System Requirements
URL	https://github.com/waldronlab/curatedMetagenomicData
Bug Reports	https://github.com/waldronlab/curatedMetagenomicData/issues

Suggests	BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan, OmicsMLRepoR, lefser
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	CrcBiomeScreen, lefser, MMUPHin, OMA, OmicsMLRepoR
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	curatedMetagenomicData_3.20.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/curatedMetagenomicData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/curatedMetagenomicData
Package Short Url	https://bioconductor.org/packages/curatedMetagenomicData/
Package Downloads Report	Download Stats