Question

Download Geo Samples Table

1

Entering edit mode

11.0 years ago

Irsan ★ 7.8k

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 • 6.2k views

ADD COMMENT • link updated 7.3 years ago by Biostar 20 • written 11.0 years ago by Irsan ★ 7.8k

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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.

ADD REPLY • link 11.0 years ago by Neilfws 49k

score 3 · Answer 1 · 2013-05-03

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11.0 years ago

AndreiR ▴ 260

Think GEOquery and GEOmetadb from Bioconductor could help.

ADD COMMENT • link 11.0 years ago by AndreiR ▴ 260

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GEOmetadb does the trick, thanks!

ADD REPLY • link 11.0 years ago by Irsan ★ 7.8k

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Glad you can make it!

ADD REPLY • link 11.0 years ago by AndreiR ▴ 260