Question: How to download all the possible RNA-seq data sets from public data bases?
gravatar for Naim.Mahi
4.4 years ago by
University of Cincinnati College of Medicine, Cincinnati, OH, USA
Naim.Mahi40 wrote:

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.

sequencing rna-seq next-gen R geo • 1.1k views
ADD COMMENTlink modified 4.4 years ago by Ar990 • written 4.4 years ago by Naim.Mahi40
gravatar for Ar
4.4 years ago by
United States
Ar990 wrote:

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!

ADD COMMENTlink written 4.4 years ago by Ar990
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