Question: How to download all the possible RNA-seq data sets from public data bases?
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gravatar for Naim.Mahi
3.0 years ago by
Naim.Mahi40
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 • 794 views
ADD COMMENTlink modified 3.0 years ago by Ar830 • written 3.0 years ago by Naim.Mahi40
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gravatar for Ar
3.0 years ago by
Ar830
United States
Ar830 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 3.0 years ago by Ar830
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