Question: Per Cancer Bulk Download from CBioPortal
2
gravatar for dirigible2012
4.4 years ago by
dirigible2012310
European Union
dirigible2012310 wrote:

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 

cancer cbioportal • 3.4k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 4.4 years ago by dirigible2012310
5
gravatar for B. Arman Aksoy
4.4 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

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.

ADD COMMENTlink written 4.4 years ago by B. Arman Aksoy1.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 884 users visited in the last hour