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
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.