Question: Where to find open access microbiome data for case-control comparative study?
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gravatar for stats134711
2.3 years ago by
stats1347110 wrote:

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?

ADD COMMENTlink modified 2.3 years ago by Wolfgang Huber13k • written 2.3 years ago by stats1347110
The microbiome R/Bioc package contains [three example data sets](http://microbiome.github.io/microbiome/Data.html) from published studies. These include genus-level profiling of 1006 western adults; diet swap study; and probiotic intervention study. The data is in phyloseq format but it originates from 16S based phylogenetic HITChip microarray, not amplicon sequencing.
ADD REPLYlink written 13 months ago by Leo Lahti30
Answer: Where to find open access microbiome data for case-control comparative study?
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gravatar for Joseph Nathaniel Paulson
2.3 years ago by
United States
Joseph Nathaniel Paulson270 wrote:

Here are two that are available:

https://bioconductor.org/packages/release/data/experiment/html/msd16s.html
https://bioconductor.org/packages/release/data/experiment/html/etec16s.html

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)

ADD COMMENTlink written 2.3 years ago by Joseph Nathaniel Paulson270
Answer: Where to find open access microbiome data for case-control comparative study?
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gravatar for Wolfgang Huber
2.3 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Also the curatedMetagenomicData package, http://bioconductor.org/packages/devel/data/experiment/html/curatedMetagenomicData.html

ADD COMMENTlink written 2.3 years ago by Wolfgang Huber13k
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