curatedMetagenomicData

DOI: 10.18129/B9.bioc.curatedMetagenomicData    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see curatedMetagenomicData.

Curated Metagenomic Data of the Human Microbiome

Bioconductor version: 3.8

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 "3.5") 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	1.12.3
License	Artistic-2.0
Depends	R (>= 3.4.0), dplyr (>= 0.5.0), Biobase(>= 2.37.0), ExperimentHub(>= 1.3.0), AnnotationHub(>= 2.9.0)
Imports	utils, tidyr, magrittr, methods, S4Vectors
LinkingTo
Suggests	BiocManager, devtools, roxygen2, testthat, covr, knitr, rmarkdown, BiocCheck, BiocStyle, BiocParallel, readr, RISmed, ggplot2, metagenomeSeq, phyloseq, ape
SystemRequirements
Enhances
URL	https://github.com/waldronlab/curatedMetagenomicData
BugReports	https://github.com/waldronlab/curatedMetagenomicData/issues
Depends On Me
Imports Me
Suggests Me	HMP16SData, metavizr
Links To Me
Build Report

Package Archives

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

Source Package	curatedMetagenomicData_1.12.3.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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	http://bioconductor.org/packages/curatedMetagenomicData/
Package Downloads Report	Download Stats