Dear community,

currently I am using NCBI GEO to compare several gene expression analysis studies. To analyse my own data in R, I mostly use DESeq2 package, which requires 1) a raw count file and 2) a meta data file.

However, I did not find a straightforward way to export the raw data in a useful format that is easily compatible with DESeq2 analysis.

How do you normally export the data for analysis from NCBI GEO? Do you have any advice or is there any package that may allow me to download the data directly from NCBI GEO in a useful format compatible with the DESeq2 package? Many thanks, this would help me a lot!

With kind regards,

Ruslan