metagenomeFeatures

DOI: 10.18129/B9.bioc.metagenomeFeatures    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see metagenomeFeatures .

Exploration of marker-gene sequence taxonomic annotations

Bioconductor version: 3.13

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 "4.1") 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

PDF		Reference Manual

Details

biocViews	Annotation, ImmunoOncology, Infrastructure, Metagenomics, Microbiome, Sequencing, Software
Version	2.12.0
In Bioconductor since	BioC 3.2 (R-3.2) (6 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
Windows Binary
macOS 10.13 (High Sierra)
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