Question: Is There A Way To Do Bulk Data Download From The Cbioportal?
gravatar for RoyC
6.5 years ago by
Penn State University
RoyC140 wrote:

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!

gene mutation • 5.0k views
ADD COMMENTlink modified 6.5 years ago by B. Arman Aksoy1.2k • written 6.5 years ago by RoyC140

have you tried cgds (R package) ?

ADD REPLYlink written 6.5 years ago by henryvuong770
gravatar for B. Arman Aksoy
6.5 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

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:

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.

ADD COMMENTlink written 6.5 years ago by B. Arman Aksoy1.2k
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