cBioPortal: Is it possible to programmatically download the tables containing mutations, structural variants and CNAs shown in the summary section of an specific patient?
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6 weeks ago

Hello everyone!

I'm currently working with the TCGA-BRCA dataset, using the data provided by both GDC Portal and cBioPortal.

There is some processed data displayed in cBioPortal that I cannot seem to download through the API.

Let me show you an example using patient TCGA-3C-AAAU.

In this webpage:

https://www.cbioportal.org/patient/summary?studyId=brca_tcga_pan_can_atlas_2018&caseId=TCGA-3C-AAAU

you can find three tables containing information on point mutations, SV and CNAs for that particular patient. Two columns that appear in "Mutations" and "CNAs" are of my special interest: mRNA Expr and Cohort.

Example

On the top right of each table there is a button that allows the user to download said tables, but the columns I am interested in aren't in the TSV file.

One option could be to obtain this information using web scrapping, but if the same could be achieved through the API or using another less time-consuming method, I'd beforever grateful to the fellow bioinformatician who helped me out.

Cheers!

download cBioPortal API web scrapping • 372 views
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