Question: Does anyone know good open data sources for metagenomic data linked to a given condition?
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gravatar for edward.messick
15 days ago by
edward.messick40 wrote:

I'm looking for either a database (like SRA) or even a study that provides its data that has labels associated with the data. Ideally, this would be metagenomic data (either sequences or abundance tables) in a study that has a strong link between a feature like a species and the condition being studied.

Just reaching out because I haven't been able to find any studies that have enough data for my application (implementing machine learning algorithms) - so ideally we are talking about at least 100 samples for the condition being studied (controls, maybe the same).

Any help is appreciated. Thanks guys

ADD COMMENTlink modified 11 days ago by erictleung90 • written 15 days ago by edward.messick40
1
gravatar for toralmanvar
15 days ago by
toralmanvar10
toralmanvar10 wrote:

Hi Edward,

You can check below mentioned post. It may solve your purpose http://github.com/gjospin/PhyloSift/issues/59.

ADD COMMENTlink written 15 days ago by toralmanvar10

thanks! I'll look through that post... of course I'm probably being a little too nitpicky with my search... we'll never really find ideal data in the real world, will we?

ADD REPLYlink written 14 days ago by edward.messick40
0
gravatar for erictleung
11 days ago by
erictleung90
United States
erictleung90 wrote:

The closest databases I can think of are

The American Gut project has the quantity of data, so that might be the most interest to you for machine learning purposes. Good luck.

ADD COMMENTlink written 11 days ago by erictleung90
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