curatedMetagenomicData

DOI: 10.18129/B9.bioc.curatedMetagenomicData    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see curatedMetagenomicData.

Curated Metagenomic Data of the Human Microbiome

Bioconductor version: 3.12

The curatedMetagenomicData package provides microbial taxonomic, functional, and gene marker abundance for samples collected from different bodysites.

Author: Lucas Schiffer <schiffer.lucas at gmail.com>, Edoardo Pasolli <edoardo.pasolli at unitn.it>, Levi Waldron <lwaldron.research at gmail.com>, Faizan Malik <faizankmalik2012 at yahoo.com>, Nicola Segata <nicola.segata at unitn.it>, Valerie Obenchain <Valerie.Obenchain at roswellpark.org>, Morgan Martin <martin.morgan at roswellpark.org>

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

Installation

To install this package, start R (version "4.0") 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	1.20.0
License	Artistic-2.0
Depends	R (>= 4.0.0), AnnotationHub(>= 2.9.0), Biobase(>= 2.37.0), dplyr (>= 0.5.0), ExperimentHub(>= 1.3.0)
Imports	magrittr, methods, S4Vectors, tidyr, utils
LinkingTo
Suggests	ape, covr, BiocCheck, BiocManager, BiocParallel, BiocStyle, devtools, ggplot2, knitr, metagenomeSeq, phyloseq, readr, RISmed, rmarkdown, roxygen2, testthat
SystemRequirements
Enhances
URL	https://github.com/waldronlab/curatedMetagenomicData
BugReports	https://github.com/waldronlab/curatedMetagenomicData/issues
Depends On Me
Imports Me
Suggests Me	HMP16SData, lefser, metavizr, MMUPHin
Links To Me
Build Report

Package Archives

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

Source Package	curatedMetagenomicData_1.20.0.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