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Extract GEO for certain experiment type

Dear all,

Suppose I have a big list of GEO's corresponding certain experiment type (e.g., sc-RNA-seq).

How can I extract all GEO's for target experiment type (sc-RNA-seq, in this case) and, after comparison all available GEO with my list, extract direct links for files which are presented in selected GEO's.

I will be very grateful if you answer at least the first question.

geo gsm geo accession bioconductor
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written by mariafirulevabio • mariafirulevabio

1 answer

Try this.

  1. Visit this link at GEO.
  2. Under Summary on the search page change to Summary text. Adjust number of results (~3256 at moment) and get results.
  3. Grep Accession numbers.
  4. Compare to your list using comm unix util.
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written by GenoMax GenoMax

Hi genomax,

Thanks for your advice. I suppose I should not only 'scRNAseq' but other terms because after intersection my list (1315 elements) with the got list from I found only 4 common accession numbers.

Could you prompt me how I can get direct links to files that correspond to the accession numbers that are not in my original list?

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written by mariafirulevabio • mariafirulevabio

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