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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: