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In publications the GEO code is usually shared and not the BioProject/study code.

I want to get the BioProject/Study Accession code of a GEO dataset (to later download the data from ENA).
I know that I can go to the website and see find it but I would like to automate the process.

GEOquery didn't provide it, and the data doesn't seem to be available via the FTP.
Is there a programmatic way to obtain it?

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  • $\begingroup$ This must be doable because it has an API here rdrr.io/bioc/GEOquery/api - which is exactly what is needed here $\endgroup$
    – M__ ♦
    Commented Apr 28, 2023 at 12:41
  • $\begingroup$ Can you please explain more about why going to the website is not good enough? For a single GEO dataset, it would be quicker and easier to use the website. $\endgroup$
    – gringer ♦
    Commented Apr 29, 2023 at 23:29
  • $\begingroup$ Because I want to download the files from multiple GEO datasets and match the data with other information. The background history is that my group currently do not have a local copy of some data which I know was published in a paper, that paper has several GEOs and I want to download them and find which samples are from the missing data. I think I identified the relevant one, but I might have missed it and I want to have a solution for the future (I think this will happen more :( ) $\endgroup$
    – llrs
    Commented May 2, 2023 at 10:05

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