12 weeks ago by
Hasso Plattner Institute, Potsdam, Germany
As far as I know for the GDC, you can only query the data with parameters like study group, sample type, platform, and specific barcodes as the files are only available sample-wise (I suppose it is the same for all the other sources where you can download the data). I am afraid that you have to implement a custom solution for yourself, first downloading the data (e.g. according to your critieria only tumor samples of specific study groups), doing the preprocessing and then selecting the genes you want to keep. This can be automized in an R script (I did this myself, only without selecting specific genes), but takes of course some time to set it up if you want to keep it flexible.