How can I programmatically download the GEO DataSets of a given accession?

Question

[James Ashmore]

I would like to download all the .sra files associated with this experiment (GSE55335). I can do it manually via the website but would like to be able to download them from a script or a terminal. I've downloaded and tried both the sra-toolkit and Entrez direct, but I've not managed to use either successfully for this task. Thank you.

[PoGibas]

Have you tried GEOquery from the Bioconductor?

Answer 1

[Ying W]

Have a look at How to download raw sequence data from GEO/SRA

Answer 2

[Sean Davis]

The SRAdb Bioconductor package is useful for this type of thing.

[tg]

You can do it with R bioconductor. just google it you will see package to load and example on how you can get it done. i will also recommend you download R in a nutshell there is exact example there.