Per Cancer Bulk Download from CBioPortal

Question

[dirigible2012]

I would like to download the mRNA expression z-scores for all genes (in all patients, with all cancers) from CBioPortal. I've found the download page, but I have to enter a list of genes I want the z-scores for - I don't want particular genes, I want to download all of them.

This data is normally available from the TCGA, but in this case I understand the z-scores are calculated from TCGA data by CBioPortal, and I'd rather not recalculate them myself. Is it possible to do a bulk download of all z-scores from CBioPortal?

Thanks for any help,

Stephanie

Answer 1

[B. Arman Aksoy]

cBioPortal, unfortunately, does not support such bulk-download requests. As you also mentioned, you can download these data sets from TCGA; since you want to work with higher-level data, I suggest you download the data from Firehose analysis results instead of using TCGA's raw data download site:

http://gdac.broadinstitute.org/

More information is available on this web site, but you might want to check out the firehose-get tool, which will let you script your downloads in an easy manner.