DOI: 10.18129/B9.bioc.metagenomeFeatures    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see metagenomeFeatures.

Exploration of marker-gene sequence taxonomic annotations

Bioconductor version: 3.8

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>

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


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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


biocViews Annotation, ImmunoOncology, Infrastructure, Metagenomics, Microbiome, Sequencing, Software
Version 2.2.3
In Bioconductor since BioC 3.2 (R-3.2) (3.5 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)
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)
Depends On Me
Imports Me greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb
Suggests Me
Links To Me
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