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>

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

Installation

To install this package, start R (version "3.5") 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 PDF
NEWS Text

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
System Requirements
URL https://github.com/waldronlab/curatedMetagenomicData
Bug Reports https://github.com/waldronlab/curatedMetagenomicData/issues
See More
Suggests BiocManager, devtools, roxygen2, testthat, covr, knitr, rmarkdown, BiocCheck, BiocStyle, BiocParallel, readr, RISmed, ggplot2, metagenomeSeq, phyloseq, ape
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me HMP16SData, metavizr
Links To Me
Build Report 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 https://bioconductor.org/packages/curatedMetagenomicData/
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