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 is the development version of metagenomeFeatures; for the stable release version, see metagenomeFeatures.

Exploration of marker-gene sequence taxonomic annotations

Bioconductor version: Development (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>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.11.1
In Bioconductor since BioC 3.2 (R-3.2) (5.5 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
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

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