metagenomeFeatures

DOI: 10.18129/B9.bioc.metagenomeFeatures    

Exploration of marker-gene sequence taxonomic annotations

Bioconductor version: Release (3.6)

metagenomeFeatures was developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.

Author: Nathan D. Olson, Joseph Nathaniel Paulson, Hector Corrada Bravo

Maintainer: Nathan D. Olson <nolson at umiacs.umd.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("metagenomeFeatures")

Documentation

HTML	R Script	Example 16S Annotation Workflow
HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Infrastructure, Metagenomics, Microbiome, Sequencing, Software
Version	1.10.0
In Bioconductor since	BioC 3.2 (R-3.2) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.4), Biobase(>= 2.17.8)
Imports	Biostrings(>= 2.36.4), ShortRead(>= 1.26.0), dplyr (>= 0.7.0), dbplyr (>= 1.0.0), stringr (>= 1.0.0), lazyeval (>= 0.1.10), RSQLite (>= 1.0.0), magrittr (>= 1.5), methods (>= 3.3.1), lattice (>= 0.20.33), metagenomeSeq(>= 1.14.2), ape (>= 3.5), purrr (>= 0.2.2)
LinkingTo
Suggests	knitr (>= 1.11), msd16s(>= 0.102.0), testthat (>= 0.10.0), rmarkdown (>= 1.3)
SystemRequirements
Enhances
URL	https://github.com/HCBravoLab/metagenomeFeatures
BugReports	https://github.com/HCBravoLab/metagenomeFeatures/issues
Depends On Me
Imports Me	greengenes13.5MgDb
Suggests Me
Build Report

Package Archives

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

Source Package	metagenomeFeatures_1.10.0.tar.gz
Windows Binary	metagenomeFeatures_1.10.0.zip
Mac OS X 10.11 (El Capitan)	metagenomeFeatures_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/metagenomeFeatures
Package Short Url	http://bioconductor.org/packages/metagenomeFeatures/
Package Downloads Report	Download Stats