Download Geo Samples Table

Question

[Irsan]

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?

[Neilfws]

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.

Answer 1

[AndreiR]

Think GEOquery and GEOmetadb from Bioconductor could help.

[Irsan]

GEOmetadb does the trick, thanks!

[AndreiR]

Glad you can make it!