Is There A Way To Do Bulk Data Download From The Cbioportal?

Question

[RoyC]

Is there anyway to download the mutation data for a gene on CBioPortal at once? I mean as opposed to selecting each tissue type one by one and copying the mutation data from there. Thank you!

[henryvuong]

have you tried cgds (R package) ? http://www.cbioportal.org/public-portal/cgds_r.jsp

Answer 1

[B. Arman Aksoy]

Unfortunately, no; we currently do not support it; but that is mostly due to the fact that TCGA already provides this through their GDAC system where you can download the latest Firehose output: http://confluence.broadinstitute.org/display/GDAC/Home

You can download data sets in a batch, for example using Broad's firehose_get tool -- or you can simply use our web service or R/Matlab clients to extract data from cBioPortal.

I hope these options will help.