I would like to do a comparative study of some methods that require human microbiome data from two groups, preferably healthy controls and diseased cases. Does anyone know of available datasets that are already in OTU table format and are of reasonable size whether it is through R packages or other sources?
Here are two that are available:
Within metagenomeSeq (https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html) there are also two smaller datasets that can be loaded with data(mouseData) or data(lungData)
Also the curatedMetagenomicData package, http://bioconductor.org/packages/devel/data/experiment/html/curatedMetagenomicData.html