Installing curatedMetagenomicData should be done through the Bioconductor package manager
biocLite(). Note that accessing the most recent datasets requires the development version of Bioconductor. Trying to install the development version of curatedMetagenomicData on top of the release version of Bioconductor won’t allow you to access datasets that have been added since the last Bioconductor release.
Install R and Bioconductor
To install the release version, follow instructions for installing
Bioconductor from https://www.bioconductor.org/install/.
To install the development version, follow the instructions at http://bioconductor.org/developers/how-to/useDevel/.
This is the usual way to install curatedMetagenomicData and is preferred in most cases. You must have Bioconductor installed already.
If you are running the development version of Bioconductor, you can also install directly from Github for the “bleeding edge” version, which may contain bugs:
From within R
curatedMetagenomicData and its related data can be accessed through R using Bioconductor and ExperimentHub.
The recommended way to access data from within R is with the
curatedMetagenomicData() function. For example:
help(package="curatedMetagenomicData")for all datasets and available functions
?curatedMetagenomicDatafor more options to this function, including whether to return relative abundances or counts, conversion of taxonomic tables to phyloseq objects, and versioning
View(combined_metadata)for a table of all participants and their annotations. See the package vignette for additional instructions, and vignettes/extras for code to reproduce results of our manuscript.
Command line usage
Set up curatedMetagenomicData as above, then use the shell script provided in the inst/commandline package directory. This script generates tab-separated value files and takes similar arguments to the R function.