curatedMetagenomicData

DOI: 10.18129/B9.bioc.curatedMetagenomicData    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see curatedMetagenomicData.

Curated Metagenomic Data of the Human Microbiome

Bioconductor version: 3.13

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]

Maintainer: Lucas schiffer <schiffer.lucas at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	curatedMetagenomicData
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch
Version	3.0.10
License	Artistic-2.0
Depends	R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment
Imports	AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, purrr, rlang, stringr, tibble, tidyr, tidyselect
LinkingTo
Suggests	BiocStyle, DT, knitr, mia, readr, rmarkdown, scater, testthat, utils, uwot, vegan
SystemRequirements
Enhances
URL	https://github.com/waldronlab/curatedMetagenomicData
BugReports	https://github.com/waldronlab/curatedMetagenomicData/issues
Depends On Me
Imports Me
Suggests Me	lefser, metavizr, MMUPHin
Links To Me
Build Report

Package Archives

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

Source Package	curatedMetagenomicData_3.0.10.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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