metagenomeFeatures

DOI: 10.18129/B9.bioc.metagenomeFeatures    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see metagenomeFeatures.

Exploration of marker-gene sequence taxonomic annotations

Bioconductor version: 3.11

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 (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("metagenomeFeatures")

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("metagenomeFeatures")

 

HTML	R Script	`metagenomeFeatures` classes and methods.
HTML	R Script	Exploring sequence and phylogenetic diversity for a taxonomic group of interest.
HTML	R Script	Using metagenomeFeatures to Retrieve Feature Data.
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ImmunoOncology, Infrastructure, Metagenomics, Microbiome, Sequencing, Software
Version	2.8.0
In Bioconductor since	BioC 3.2 (R-3.2) (5 years)
License	Artistic-2.0
Depends	R (>= 3.5), Biobase(>= 2.17.8)
Imports	Biostrings(>= 2.36.4), S4Vectors(>= 0.23.18), 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), ape (>= 3.5), DECIPHER(>= 2.4.0)
LinkingTo
Suggests	knitr (>= 1.11), testthat (>= 0.10.0), rmarkdown (>= 1.3), devtools (>= 1.13.5), ggtree(>= 1.8.2), BiocStyle(>= 2.8.2), phyloseq(>= 1.24.2), forcats (>= 0.3.0), ggplot2 (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/HCBravoLab/metagenomeFeatures
BugReports	https://github.com/HCBravoLab/metagenomeFeatures/issues
Depends On Me
Imports Me	greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	metagenomeFeatures_2.8.0.tar.gz
Windows Binary	metagenomeFeatures_2.8.0.zip
macOS 10.13 (High Sierra)	metagenomeFeatures_2.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/metagenomeFeatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/metagenomeFeatures
Package Short Url	https://bioconductor.org/packages/metagenomeFeatures/
Package Downloads Report	Download Stats