README.md

In HCBravoLab/greengenes13.5MgDb: Greengenes 13.5 16S rRNA Database Annotation Data

This is an R Bioconductor Annotation package with the greengenes 13.5 database. (https://github.com/HCBravoLab/metagenomeFeatures.git). The database data is formatted as a MgDb-class object defined in the metagenomeFeatures Bioconductor package (https://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html).

The package is available from (bioconductor)[https://bioconductor.org] https://bioconductor.org/packages/release/data/annotation/html/greengenes13.5MgDb.html.

To install the development version of the package: 1. You need to use the development version of metagenomeFeatures, which can be installed using devtools::install_github.

devtools::install_github("HCBravoLab/metagenomeFeatures")
````

2. Download the source version of the annotation package
We have provided a link to a source version of the package with the database files as the database files are too large to include in the github repository. 

wget -v -O greengenes13.5MgDb_1.9.0.tar.gz https://umd.box.com/shared/static/kfl94pacgeuwmarm0m4o7v16ipyzywgy.gz

3. Install using the downloaded file.  

install.packages("greengenes13.5MgDb_1.9.0.tgz", repo = NULL) ```

The metagenomeFeatures package has vignettes demonstrating how to work with MgDb-class objects.

HCBravoLab/greengenes13.5MgDb documentation built on May 6, 2019, 9:45 p.m.