Download Geo Samples Table · Biostar

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Download Geo Samples Table

I would like to download the complete GEO samples table. I am not interested in all the raw data of those samples but just the samples table itself. When i go to the GEO sample browser it presents a list of all the samples reported in GEO datasets. There is an export button on top of the presented table but it only allows for exporting 5000 rows at a time (there are 918,147 so that will take a while). Is there an easier way to do it?

geo

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updated 9.6 years ago by Biostar

• written 13.3 years ago by Irsan

Tricky. I don't see any files that correspond in the FTP site. Only solution I can think of is web scraping with a Mechanize library.

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written 13.3 years ago by Neilfws

1 answer

Think GEOquery and GEOmetadb from Bioconductor could help.

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written 13.3 years ago by AndreiR

GEOmetadb does the trick, thanks!

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written 13.3 years ago by Irsan

Glad you can make it!

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written 13.3 years ago by AndreiR

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