Question: fetch all relevant datasedts from GEO database
0
gravatar for APJ
4 weeks ago by
APJ20
Sweden
APJ20 wrote:

Hi,

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 • 83 views
ADD COMMENTlink written 4 weeks ago by APJ20
1

What have you tried?

ADD REPLYlink written 4 weeks ago by Kevin Blighe51k

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

ADD REPLYlink written 4 weeks ago by APJ20

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 4 weeks ago by ATpoint25k

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 4 weeks ago by APJ20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1716 users visited in the last hour