MATLAB alternative to the deprecated CGDS-R package

[John Githaka]

Hello,

I use CGDS-R package in MATLAB (webservice.do), which has recently been deprecated. Is there an alternative MATLAB package that uses cBioPortal REST API to access cBioPortal data? 

Thank you for your assistance with this.

-John

[Floris Vleugels]

Hi John,

Thank you for your question! Sadly I don't believe there are any alternative MATLAB packages at the moment. 

However, if you want to keep using MATLAB to make API calls, you might choose to use the base MATLAB functions to make http requests to the cBioPortal API pages (see here for the official MATLAB http request documentation: https://nl.mathworks.com/help/matlab/http-interface.html)

If you have any remaining questions, please feel free to reply to all.

Kind regards,

Floris Vleugels

Data Engineer

E flo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

--
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/f6df78e4-b6c8-4b35-86c5-860f74008157n%40googlegroups.com.

[de Bruijn, Ino]

Hi John,

 

Thanks for reaching out! Unfortunately we don’t provide a MATLAB package for the REST API at this stage

 

The `/webservice.do` API was deprecated in cBioPortal v6. Is there any way you can use one of the R or Python clients instead?

 

Thank you!

Ino

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of John Githaka <mar...@ualberta.ca>
Date: Wednesday, April 3, 2024 at 2:07 PM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] MATLAB alternative to the deprecated CGDS-R package

Hello, I use CGDS-R package in MATLAB (webservice. do), which has recently been deprecated. Is there an alternative MATLAB package that uses cBioPortal REST API to access cBioPortal data?  Thank you for your assistance with this. -John -- You

--

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/f6df78e4-b6c8-4b35-86c5-860f74008157n%40googlegroups.com.

=====================================================================

Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.

Disclaimer ID:MSKCC

[John Githaka]

Thanks for your help with this.

I have successfully installed the python client cbio_py (https://github.com/odagayev/cbio_py). I just wish it was better documented with some examples on how to get specific gene molecular profiles for a given study. 

For example, if I'm interest in gene "BAD" from the RNAseq profile in "brca_tcga", how would I call this using cbio_py?

[John Githaka]

UPDATE. I've found the Python client bravado to be more efficient in getting the molecular data that I am interested in (and I can call it from MATLAB if need be). While it works for all other molecular profiles such as RNA, mutations e.t.c, it unfortunately returns an empty output when I try accessing RPPA data for a gene whose RPPA data ('BAD_pS112') I'm sure is available. Any thoughts on why accessing RPPA data is failing in bravado? Below is the code I run

RPPA = cbioportal.Molecular_Data.getAllMolecularDataInMolecularProfileUsingGET(molecularProfileId="brca_tcga_rppa", sampleListId="brca_tcga_all", entrezGeneId=572).result()

Any help is greatly appreciated.

-John