metagenomeFeatures

This package is for version 3.9 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: 3.9

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")
`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. HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, ImmunoOncology, Infrastructure, Metagenomics, Microbiome, Sequencing, Software
Version 2.4.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License Artistic-2.0
Depends R (>= 3.5), Biobase(>= 2.17.8)
Imports Biostrings(>= 2.36.4), S4Vectors(>= 0.14.7), 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)
System Requirements
URL https://github.com/HCBravoLab/metagenomeFeatures
Bug Reports https://github.com/HCBravoLab/metagenomeFeatures/issues
See More
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)
Linking To
Enhances
Depends On Me
Imports Me greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package metagenomeFeatures_2.4.0.tar.gz
Windows Binary metagenomeFeatures_2.4.0.zip
Mac OS X 10.11 (El Capitan) metagenomeFeatures_2.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/metagenomeFeatures
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metagenomeFeatures
Bioc Package Browser https://code.bioconductor.org/browse/metagenomeFeatures/
Package Short Url https://bioconductor.org/packages/metagenomeFeatures/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive