Hello!
I have a list of PMIDs and would like to query GEOquery and SRAdb to see if there is data submitted from these papers, and if submitted, I would like to download.
As I haven't received any response on https://support.bioconductor.org/p/115547/, I am posting my question here.
The NCBI elink utility will take a list of PMIDs as input and map to GEO GDS, or SRA accessions. For example, here are 2 PMIDs that each have one associated GEO GDS:
This call returns the GDS IDs corresponding to each PMID. To search in SRA, use db=sra instead of db=gds.
You'd then use the returned GEO GDS or SRA IDs to retrieve data from GEO or SRA. To do this you could use R GEOquery or perhaps the SRA toolkit.
Depending on your data/application you could script the steps above.
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