curatedMetagenomicData
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see curatedMetagenomicData.
Curated Metagenomic Data of the Human Microbiome
Bioconductor version: 3.19
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("curatedMetagenomicData")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch |
| Version | 3.12.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment |
| Imports | AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia, purrr, rlang, stringr, tibble, tidyr, tidyselect |
| System Requirements | |
| URL | https://github.com/waldronlab/curatedMetagenomicData |
| Bug Reports | https://github.com/waldronlab/curatedMetagenomicData/issues |
See More
| Suggests | BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MMUPHin, lefser |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | curatedMetagenomicData_3.12.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/curatedMetagenomicData |
| Source Repository (Developer Access) | git clone [email protected]:packages/curatedMetagenomicData |
| Package Short Url | https://bioconductor.org/packages/curatedMetagenomicData/ |
| Package Downloads Report | Download Stats |