Question: Is There A Way To Do Bulk Data Download From The Cbioportal?
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gravatar for RoyC
5.7 years ago by
RoyC140
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 • 4.5k views
ADD COMMENTlink modified 5.7 years ago by B. Arman Aksoy1.2k • written 5.7 years ago by RoyC140
1

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

ADD REPLYlink written 5.7 years ago by henryvuong750
2
gravatar for B. Arman Aksoy
5.7 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: 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.

ADD COMMENTlink written 5.7 years ago by B. Arman Aksoy1.2k
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