Our dataset includes more than 168,000 samples of publicly available 16S rRNA amplicon sequencing data, all processed using the same pipeline and reference database.
The goal of the MicroBioMap package is simply to expose these data to the broad community of Bioconductor and R users with the smallest fuss possible.
See the vignette for more details.
For the smoothest installation experience, use the BiocManager Bioconductor
package.
BiocManager::install('blekhmanlab/MicroBioMap')
Load the compendium using:
library(MicroBioMap)
cpd <- getCompendium()
The resulting object is a TreeSummarizedExperiment object. Currently, the
"tree" part of the TreeSummarizedExperiment is not populated, but that is
on the roadmap.
After loading the compendium, you will have immediate access to nearly 170,000 microbiome samples.
The getCompendium function retrieves data stored by Zenodo and accepts an optional parameter indicating which version to download—for example, getCompendium('1.0.1'). Version 1.1.0 is retrieved by default.