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cBioPortal for Cancer Genomics Discussion Group

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1–30 of 5054

This mailing list is for questions that are related to cbioportal.org. In order to filter out spams, every message is moderated. If you don't see your message posted immediately, it will be moderated and posted later.

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Jones, Brett C (kqt4tu), Benjamin Gross4

Feb 8

log2CNA derivation

Hi Brett, That's a good question. I did some further searching and found this page on the GDC

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log2CNA derivation

Hi Brett, That's a good question. I did some further searching and found this page on the GDC

Feb 8

Tejaswi Patil, Ph.D., … HIROMI YANASE10

Feb 6

Uploading public data

Hello Benjamin, Thank you for your reply. I could view Ritika's response. I'm looking forward

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Uploading public data

Hello Benjamin, Thank you for your reply. I could view Ritika's response. I'm looking forward

Feb 6

Mariana Gomes Da Silva Araujo, … Benjamin Gross6

Feb 6

What does "all samples" mean in TCGA BRCA (PanCancer) dataset?

Hi Mariana, Thanks for your patience. I see the confusion. The z-scores generated are study specific,

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What does "all samples" mean in TCGA BRCA (PanCancer) dataset?

Hi Mariana, Thanks for your patience. I see the confusion. The z-scores generated are study specific,

Feb 6

Chin Zhen Jie, … Nikolaus Schultz8

Feb 5

cBioPortal Annotation Queries

Dear Professor Schultz, Thank you for your email. Apologies for the lack of clarity in my previous

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cBioPortal Annotation Queries

Dear Professor Schultz, Thank you for your email. Apologies for the lack of clarity in my previous

Feb 5

Rye Visualization, Prasanna Jagannathan2

Feb 5

Correlating mRNA Data with Drug Response Data in cBioPortal Co-expression

Hi Tom Thanks for your question. One of the file formats that cBioPortal supports is Generic Assay.

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Correlating mRNA Data with Drug Response Data in cBioPortal Co-expression

Hi Tom Thanks for your question. One of the file formats that cBioPortal supports is Generic Assay.

Feb 5

Prashanth Bachu, Prasanna Jagannathan14

Feb 5

Error 400: Invalid Request

Hi Prashanth The Master SAML processing URL has to be the Keycloak URL and not cBioPortal. There are

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Error 400: Invalid Request

Hi Prashanth The Master SAML processing URL has to be the Keycloak URL and not cBioPortal. There are

Feb 5

Ji Hen Lau, … Prasanna Jagannathan8

Feb 5

Import New Reference Genome

Hi Jag, Thanks for the clarification! Regards, Ji Hen On Wednesday, 5 February 2025 at 08:56:05 UTC+8

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Import New Reference Genome

Hi Jag, Thanks for the clarification! Regards, Ji Hen On Wednesday, 5 February 2025 at 08:56:05 UTC+8

Feb 5

xinxin chen, Pieter Lukasse4

Feb 5

How to Logout when login with Microsoft account

Hi Xinxin, I think you will need to check this with your IDP and see if they have a logout URL that

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How to Logout when login with Microsoft account

Hi Xinxin, I think you will need to check this with your IDP and see if they have a logout URL that

Feb 5

孙露露, Prasanna Jagannathan2

Feb 4

queries on cbioportal website

Hi Lulu Sun, If the data is available on the cbioportal study, then it is possible to classify or

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queries on cbioportal website

Hi Lulu Sun, If the data is available on the cbioportal study, then it is possible to classify or

Feb 4

zedaes, Prasanna Jagannathan2

Feb 3

Looking for a way to download patient specific mutations in a study

Hi Zedaes, As you correctly surmised, the data_mutations.txt file is in a format called MAF. Details

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Looking for a way to download patient specific mutations in a study

Hi Zedaes, As you correctly surmised, the data_mutations.txt file is in a format called MAF. Details

Feb 3

Kilroy, Mary (kilroymk), Prasanna Jagannathan2

Jan 31

Hi Mary For Genie data, please use the URL https://genie.cbioportal.org You can submit a request to

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Hi Mary For Genie data, please use the URL https://genie.cbioportal.org You can submit a request to

Jan 31

aghil hooshmand, Prasanna Jagannathan2

Jan 31

Error in Comparison & Download Tabs When Selecting just Methylation Profile

Hi Aghil, Can you elaborate in detail on the steps you took with the public study brca_tcga_pub2015?

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Error in Comparison & Download Tabs When Selecting just Methylation Profile

Hi Aghil, Can you elaborate in detail on the steps you took with the public study brca_tcga_pub2015?

Jan 31

Prashanth Bachu, Benjamin Gross26

Jan 31

Error installing cbioportal with docker desktop in windows system using WSL

Hi Benjamin, Thanks for quick response. My case is not same as above that you mentioned. I was able

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Error installing cbioportal with docker desktop in windows system using WSL

Hi Benjamin, Thanks for quick response. My case is not same as above that you mentioned. I was able

Jan 31

Ishrak Hasin, Prasanna Jagannathan5

Jan 31

molecularProfileIds Error

Hi Jag, Thanks a ton for your suggestions. It was really well thought. Best, Ishrak EKFZ Dresden On

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molecularProfileIds Error

Hi Jag, Thanks a ton for your suggestions. It was really well thought. Best, Ishrak EKFZ Dresden On

Jan 31

Prashanth Bachu, Ruslan Forostianov5

Jan 30

Invalid redirect uri

Hi Ruslan, Thanks for your solution. I was able to resolve the issue by adding server.forward-headers

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Invalid redirect uri

Hi Ruslan, Thanks for your solution. I was able to resolve the issue by adding server.forward-headers

Jan 30

Ishrak Hasin, … jagn...@gmail.com4

Jan 29

Trouble uploading clinical data to local docker deployed cbioportal

Hi Ishrak Based on the error message, it seems that the data_clinical_sample.txt file does not have

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Trouble uploading clinical data to local docker deployed cbioportal

Hi Ishrak Based on the error message, it seems that the data_clinical_sample.txt file does not have

Jan 29

Ishrak Hasin, jagn...@gmail.com2

Jan 29

Error Uploading Custom Data to Local cBioPortal – Is meta_mutations.txt Required?

Hi Ishrak, For any upload, it takes both meta file and data file. In your case, there is no mutation

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Error Uploading Custom Data to Local cBioPortal – Is meta_mutations.txt Required?

Hi Ishrak, For any upload, it takes both meta file and data file. In your case, there is no mutation

Jan 29

Humphrey Gardner, jagn...@gmail.com2

Jan 29

Error report per request on page

Hi Humphrey, I have created a virtual study based on the criteria you mentioned in your email. https:

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Error report per request on page

Hi Humphrey, I have created a virtual study based on the criteria you mentioned in your email. https:

Jan 29

Alan Mackay, Pieter Lukasse3

Jan 29

Submitting a new dataset to pedcBioPortal

Thanks Pieter Yes. It's the pedcBioPortal I am interested in and I have a couple of datasets I

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Submitting a new dataset to pedcBioPortal

Thanks Pieter Yes. It's the pedcBioPortal I am interested in and I have a couple of datasets I

Jan 29

Jill Hansalia, Ruslan Forostianov2

Jan 28

cbioportal problem

Hi Jill, Thank you for your email. Could you provide additional context regarding the issue? A step-

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cbioportal problem

Hi Jill, Thank you for your email. Could you provide additional context regarding the issue? A step-

Jan 28

山口　舞子, … Nikolaus Schultz5

Jan 27

Inquiry About Lollipop Plot Generation on cBioPortal

Dear Niki, I apologize for the oversight in my previous email. I realized that I forgot to include

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Inquiry About Lollipop Plot Generation on cBioPortal

Dear Niki, I apologize for the oversight in my previous email. I realized that I forgot to include

Jan 27

Edoardo Garbo, Pieter Lukasse3

Jan 27

MSKCC Chord TMB

Dear Pieter -- thank you for reaching out. The team was able to upload TMB data, so now I am all set.

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MSKCC Chord TMB

Dear Pieter -- thank you for reaching out. The team was able to upload TMB data, so now I am all set.

Jan 27

Ji Hen Lau, Ruslan Forostianov2

Jan 27

study_es_0 and deployment with Docker

Hi Ji Hen Lau, The study_es_0 is no longer included as a test data within the Docker image and the

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study_es_0 and deployment with Docker

Hi Ji Hen Lau, The study_es_0 is no longer included as a test data within the Docker image and the

Jan 27

chen512584130, … Aaron L4

Jan 27

cBioPortal user reported error

HI Walid, Thanks for the alert. The service we use for that column has changed a little and we have

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cBioPortal user reported error

HI Walid, Thanks for the alert. The service we use for that column has changed a little and we have

Jan 27

Xiuzhen Chen, Pieter Lukasse4

Jan 25

How to retrieve the exact information of protein fusion events

Hi Xiuzhen, Good question. There is some documentation about this data format that you can find here

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How to retrieve the exact information of protein fusion events

Hi Xiuzhen, Good question. There is some documentation about this data format that you can find here

Jan 25

Shen, Jie (cua9zd), de Bruijn, Ino4

Jan 25

Dear Sir: Thanks a lot for your reply and help! I saw lots of minus RNA expression value when I check

unread,

Dear Sir: Thanks a lot for your reply and help! I saw lots of minus RNA expression value when I check

Jan 25

Matteo Valerio, Gaofei Zhao4

Jan 24

Error During cBioPortal Deployment with Docker on Windows

Hi Gaofei, I've successfully installed wget and executed the .init.sh script, but unfortunately,

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Error During cBioPortal Deployment with Docker on Windows

Hi Gaofei, I've successfully installed wget and executed the .init.sh script, but unfortunately,

Jan 24

J. N, de Bruijn, Ino3

Jan 24

Determination of mutation on which Chromsome

Apologies – replied to the wrong thread For determining homozygosity, there's an explanation in

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Determination of mutation on which Chromsome

Apologies – replied to the wrong thread For determining homozygosity, there's an explanation in

Jan 24

J. N, de Bruijn, Ino2

Jan 24

MSI Score cutoff

Hi JD, Thanks for reaching out! The MSI Score you are referring to: in which study on the cBioPortal

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MSI Score cutoff

Hi JD, Thanks for reaching out! The MSI Score you are referring to: in which study on the cBioPortal

Jan 24

Saxena, Anurag, Gaofei Zhao2

Jan 24

Cancer Type and Cancer Type Detailed for Samples with ICD-O Site code only (no morphology) in a private study hosted on a private cbioportal instance

Hi Anurag, The morphology codes are required to get the right mappings, we can't get correct

unread,

Cancer Type and Cancer Type Detailed for Samples with ICD-O Site code only (no morphology) in a private study hosted on a private cbioportal instance

Hi Anurag, The morphology codes are required to get the right mappings, we can't get correct

Jan 24

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