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
<p>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 <a href="http://gdac.broadinstitute.org/">Firehose analysis results </a>instead of using TCGA&#39;s raw data download site:</p>

<p>http://gdac.broadinstitute.org/</p>

<p>More information is available on this web site, but you might want to check out the <a href="https://confluence.broadinstitute.org/display/GDAC/Download">firehose-get</a> tool, which will let you script your downloads in an easy manner.</p>
