R package for annotating metagenomic datasets with taxonomic information
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metagenomeFeatures is an R package with annotating 16S metagenomic sequence data using the metagenomeFeatures package (https://github.com/HCBravoLab/metagenomeFeatures.git). A package for the greengenes database version 13.5 was developed, greengenes13.5MgDb(https://github.com/HCBravoLab/greengenes13.5MgDb), for annotating 16S datasets using metagenomeFeatures.
This package is available on Bioconductor, https://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html.

We are working on version 2.0, which includes significant updates to the MgDb and mgFeatures class definitions.

To install the development version of the package

  • this can be done using devtools install_github("HCBravoLab/metagenomeFeatures")

See the greengenes13.5MgDb github repository, https://github.com/HCBravoLab/greengenes13.5MgDb, for instructions to instal the development version of the annotation package.

The package has vignettes demonstrating how to use the greenegenes13.5MgDb package to annotate 16S metagenomic sequence data.