How to download all the possible RNA-seq data sets from public data bases?

Question

[Naim.Mahi]

Dear all,

I want to write a function in R that will download all possible RNA-Seq data sets and sample annotations from public data bases such as GEO. Is there any package that will do it? I know SRAdb or GEOquery but I need to provide SRR or GSM number. I would really appreciate any help regarding this issue. TIA.

Answer 1

[ATRX]

Use SRA Run Selector. This will provide you the SRA run table. And, then for download use sra-dump and then write a small script & automate the process. Good luck!