Question

Where to find open access microbiome data for case-control comparative study?

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stats134711 • 0

@stats134711-12832

Last seen 7.6 years ago

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?

microbiome data analysis data request • 1.8k views

ADD COMMENT • link updated 7.6 years ago by Wolfgang Huber ★ 13k • written 7.6 years ago by stats134711 • 0

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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 REPLY • link 6.5 years ago Leo Lahti ▴ 40

score 0 · Answer 1 · 2017-04-13

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)

score 0 · Answer 2 · 2017-04-14

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Wolfgang Huber ★ 13k

@wolfgang-huber-3550

Last seen 3 months ago

EMBL European Molecular Biology Laborat…

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

ADD COMMENT • link 7.6 years ago Wolfgang Huber ★ 13k