microbiomeData

An R package containing all of the curated datasets from MicrobiomeDB.org and a helper function to list which datasets are available.

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Installation

Use the R package remotes to install microbiomeData. From the R command prompt:

remotes::install_github('microbiomeDB/microbiomeData')

Usage

This package contains all of the curated datasets from MicrobiomeDB.org. It is an extension to the MicrobiomeDB R package which can be used to analyze and visualize these data. That package is installed and attached with this one.

Direct Usage

You can get a list of all curated datasets available within this package by doing the following:

microbiomeData::getCuratedDatsetNames()
myData <- microbiomeData::DiabImmune

Once you have your favorite dataset as myData, you can ask for specific collections from that dataset. A collection is any group of variables that represent a biologically coherent concept and are measured over a comparable range. Relative abundances at a specific taxonomic rank are an example. That might look something like:

getCollectionNames(myData) # will print the names of collections
myCollection <- getCollection(myData, '16S (V4) Species')

License

Apache 2.0