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curatedMetagenomicData

This is the development version of curatedMetagenomicData; for the stable release version, see curatedMetagenomicData.

Curated Metagenomic Data of the Human Microbiome

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("curatedMetagenomicData")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch
Version 3.9.0
License Artistic-2.0
Depends R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment
Imports AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia, purrr, rlang, stringr, tibble, tidyr, tidyselect
Linking To
Suggests BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan
System Requirements
Enhances
URL https://github.com/waldronlab/curatedMetagenomicData
Bug Reports https://github.com/waldronlab/curatedMetagenomicData/issues
See More
Depends On Me
Imports Me
Suggests Me lefser, MMUPHin
Links To Me
Build Report  

Package Archives

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

Source Package curatedMetagenomicData_3.9.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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/
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