Question: fetch all relevant datasedts from GEO database
gravatar for APJ
11 months ago by
APJ30 wrote:


I would like to retrieve relevant studies available on GEO database for my search terms.

For example: I am interested in RNA-seq datasets published for a particular gene X which has a role in kidney disease. The experimental design should include control and study group with minimum of10 replicate samples.

How do I fetch relevant GEOseries using ncbi-eutils? Any ideas please?

eutils ncbi geo • 204 views
ADD COMMENTlink written 11 months ago by APJ30

What have you tried?

ADD REPLYlink written 11 months ago by Kevin Blighe65k

I tried the hard way through the GEO DataSets Advanced Search Builder, which takes multiple query terms to fetch the results.

ADD REPLYlink written 11 months ago by APJ30

By best knowledge there is no ready-to-use approach that is that specific and frees you from the unpleasant manual search. You will have to do it the old-fashioned way, using PubMed, google and tools like sra-explorer plus a lot of individual effort.

ADD REPLYlink written 11 months ago by ATpoint38k

Yes, I was doing the manual search. But interested to know, if there is any easy and better way of searching. Thanks for sra-explorer link!

ADD REPLYlink written 11 months ago by APJ30
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