Downloading the data

Hoda Kardooni

unread,

May 26, 2022, 8:44:05 AM5/26/22

to cbiop...@googlegroups.com

Hello,

I hope you are doing well.

I was wondering if it is possible to download the comprehensive data including the drugs and response (Oncokb) related to each variant from Genie cbioportal? Also why when I click on the Matlab/R tab, It is not working?

Thanks,

BW,

Hoda

David Higgins

unread,

May 26, 2022, 9:26:13 AM5/26/22

to Hoda Kardooni, cbiop...@googlegroups.com

Hi Hoda,

You can download all the data for an individual study by clicking the “Download” button next to the study name. You can also download information after you submit your query as well, using the Download dropdown on the OncoPrint page. There’s also a Download tab with multiple download options. See the attached screenshot

The Matlab/R tab links out to our documentation on how to access cBioPortal data via your own Matlab/R environment (https://docs.cbioportal.org/web-api-and-clients/#r-client). Let us know if you’re unable to see the link.

Best,

David M. Higgins, Ph.D. | (he/him)
Informatics Program Manager
Center for Data-Driven Discovery in Biomedicine (D3b)
Children’s Hospital of Philadelphia, USA

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CWLP265MB5771BF6350BB7E412CF90299ECD69%40CWLP265MB5771.GBRP265.PROD.OUTLOOK.COM.

cbioportal-download-options.png

David Higgins

unread,

May 26, 2022, 10:08:22 AM5/26/22

to H Ka, cBioPortal for Cancer Genomics Discussion Group

Hi Hoda,

At this time there’s no way to download the OncoKB data out of cBioPortal. The best way to do this would be to access it via OncoKB’s website (https://www.oncokb.org/) and merge these annotations locally.

Best,

David M. Higgins, Ph.D. | (he/him)
Informatics Program Manager
Center for Data-Driven Discovery in Biomedicine (D3b)
Children’s Hospital of Philadelphia, USA

From: H Ka <hodaka...@googlemail.com>
Date: Thursday, May 26, 2022 at 9:56 AM
To: David Higgins <da...@d3b.center>
Subject: Private message regarding: [cbioportal] Downloading the data

Hello David,

Thanks for the reply.

I tried downloading some data but it does not give me the drugs or drug affects (response/resistance). I was wondering if it is possible to download this data too. please have a look at the attached pic. In the annotation tab when I download the data, it just gives me some description. I would like to download the associated drug to each alteration too if possible.