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cBioPortal for Cancer Genomics Discussion Group

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Sreekumar, Nitin, Gaofei Zhao2

Dec 15

cBioportal API issue

Hi Nitin, Thank you for reporting this issue. I have filed a ticket for it here. We will look into

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cBioportal API issue

Hi Nitin, Thank you for reporting this issue. I have filed a ticket for it here. We will look into

Dec 15

Ahsen Tahir, Gaofei Zhao2

Dec 15

Inquiry Regarding Availability of cBioPortal API Tokens

Hi Ahsen, Thanks for reaching out. API tokens are still supported on authorized cBioPortal instances.

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Inquiry Regarding Availability of cBioPortal API Tokens

Hi Ahsen, Thanks for reaching out. API tokens are still supported on authorized cBioPortal instances.

Dec 15

Jun mei Hu Frisk, JJ Gao2

Dec 15

a question about figure on "Survival" based on mRNA expression

Hi Jun Mei, Thanks for reaching out to me. Both use the Kaplan–Meier method, a standard way to plot

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a question about figure on "Survival" based on mRNA expression

Hi Jun Mei, Thanks for reaching out to me. Both use the Kaplan–Meier method, a standard way to plot

Dec 15

Dec 15

Tissue Sample Image files for local cbio instance (?)

Hi John, That should work. If not, please let us know if some details of the issue. You might find

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Tissue Sample Image files for local cbio instance (?)

Hi John, That should work. If not, please let us know if some details of the issue. You might find

Dec 15

Carlos Espinosa, … Sachin Kumar3

Dec 13

Unable to deploy version 5 of cbioportal

I can help if you need On Thu, Dec 11, 2025 at 9:56 AM Gaofei Zhao <zhaoga...@gmail.com>

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Unable to deploy version 5 of cbioportal

I can help if you need On Thu, Dec 11, 2025 at 9:56 AM Gaofei Zhao <zhaoga...@gmail.com>

Dec 13

Aaron Gmail, de Bruijn, Ino2

Dec 11

Thanks for reaching out, Aaron! Appreciate your offer to help test the chat agent! The chat interface

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Thanks for reaching out, Aaron! Appreciate your offer to help test the chat agent! The chat interface

Dec 11

Leal, Alessandro, Benjamin Gross9

Dec 11

Issue Accessing GENIE API With Data Access Token (Redirects to Google Login)

Ok great, thank you! -B On Dec 11, 2025, at 2:41 PM, Leal, Alessandro <Alessandro.Leal@nyulangone.

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Issue Accessing GENIE API With Data Access Token (Redirects to Google Login)

Ok great, thank you! -B On Dec 11, 2025, at 2:41 PM, Leal, Alessandro <Alessandro.Leal@nyulangone.

Dec 11

Dr. Pushpita Roy, Nikolaus Schultz3

Dec 10

For Suggestions

Dear Niki, Thank you so much for your reply. I really appreciate! Best Regards, DR. Pushpita Roy MBBS

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For Suggestions

Dear Niki, Thank you so much for your reply. I really appreciate! Best Regards, DR. Pushpita Roy MBBS

Dec 10

Patrice Naud (CIUSSS EMTL), de Bruijn, Ino2

Dec 10

Requesting Access to Test cBioPortal AI Chat Interface Prototype

Hi Patrice, Thanks so much for reaching out! This work is in prototype stage, so keep expectations

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Requesting Access to Test cBioPortal AI Chat Interface Prototype

Hi Patrice, Thanks so much for reaching out! This work is in prototype stage, so keep expectations

Dec 10

Brett Gaspers, de Bruijn, Ino2

Dec 10

Chat interface access

Hi Brett, Thanks so much for reaching out! This work is in prototype stage, so keep expectations low

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Chat interface access

Hi Brett, Thanks so much for reaching out! This work is in prototype stage, so keep expectations low

Dec 10

Federico Colombo, Nikolaus Schultz2

Dec 10

DEFINITION OF MUTATION TYPE

Hi Federico, This seems to be basic molecular biology question. I found this glossary about the

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DEFINITION OF MUTATION TYPE

Hi Federico, This seems to be basic molecular biology question. I found this glossary about the

Dec 10

Alkaissi, Hussam (NIH/NIDDK) [E], … Nikolaus Schultz7

Dec 9

TCGA-PCPG Cohort

Hi Niki, I thought of that as well, and already made this list of available info. Let me know what

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TCGA-PCPG Cohort

Hi Niki, I thought of that as well, and already made this list of available info. Let me know what

Dec 9

Matthew Witek, Nikolaus Schultz2

Dec 9

Re: help with download

Hi Matthew, Unfortunately, that is not possible at the moment and is not a planned feature. I suggest

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Re: help with download

Hi Matthew, Unfortunately, that is not possible at the moment and is not a planned feature. I suggest

Dec 9

Sadie Dresman (Cardiff and Vale UHB - Awmgs), Aaron L2

Dec 9

cBioPortal user reported error

Hi Sadie, Thanks for this report. Looks like there may have been a temporary problem with our server.

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cBioPortal user reported error

Hi Sadie, Thanks for this report. Looks like there may have been a temporary problem with our server.

Dec 9

刘英, Aaron L2

Dec 9

THanks for this report. We were unable to reproduce the problem. Can you try again? --Aaron On Tue,

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THanks for this report. We were unable to reproduce the problem. Can you try again? --Aaron On Tue,

Dec 9

Dec 9

Organization Invitation - Winter of Code 5.0

Dear Team, I hope you are doing well. I am reaching out on behalf of the organising team of Winter of

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Organization Invitation - Winter of Code 5.0

Dear Team, I hope you are doing well. I am reaching out on behalf of the organising team of Winter of

Dec 9

Turski, Michelle, Benjamin Gross5

Dec 5

Request for VPAT for cBioPortal

Thanks Benjamin, FWIW, the ruling applies to "state and local government web applications"

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Request for VPAT for cBioPortal

Thanks Benjamin, FWIW, the ruling applies to "state and local government web applications"

Dec 5

Damrauer, Jeffrey, Benjamin Gross2

Dec 3

Error for bladder_msk_2025

Hi Jeff, Thanks for the email. Our curation team will be releasing this study soon. I've cc'd

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Error for bladder_msk_2025

Hi Jeff, Thanks for the email. Our curation team will be releasing this study soon. I've cc'd

Dec 3

Chen Jingxian, Benjamin Gross2

Dec 3

cbioportal AI interface

Hi Nova, Your email is timely. The cBioPortal team is in the final stages of approving an RFC to

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cbioportal AI interface

Hi Nova, Your email is timely. The cBioPortal team is in the final stages of approving an RFC to

Dec 3

Isabel.Misir, Prasanna Jagannathan2

Dec 2

Hi Izzy Based on my understanding of the article, the unit of measurement is FPKM. Link to PDF is

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Hi Izzy Based on my understanding of the article, the unit of measurement is FPKM. Link to PDF is

Dec 2

Costello, Heather, Ritika Kundra2

Nov 26

Pptc link heads-up

Hi Heather, Thanks for notifying us. The link has been updated. Ritika On Mon, Nov 24, 2025 at 4:07

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Pptc link heads-up

Hi Heather, Thanks for notifying us. The link has been updated. Ritika On Mon, Nov 24, 2025 at 4:07

Nov 26

Elena Karydi, … Guckin, Danielle14

Nov 26

cBioPortal user reported error

Hi, I don't see that as an option (the website looks different for me). I am selecting a specific

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cBioPortal user reported error

Hi, I don't see that as an option (the website looks different for me). I am selecting a specific

Nov 26

内田士朗, Prasanna Jagannathan2

Nov 25

Inquiry About Downloading “mRNA Expression Z-Score Relative to All Samples (log RNA-seq V2 RSEM)” for Breast Invasive Carcinoma (TCGA, PanCancer Atlas)

Hi Shiro Thanks for emailing the cBioPortal team. The link to the entire dataset is available next to

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Inquiry About Downloading “mRNA Expression Z-Score Relative to All Samples (log RNA-seq V2 RSEM)” for Breast Invasive Carcinoma (TCGA, PanCancer Atlas)

Hi Shiro Thanks for emailing the cBioPortal team. The link to the entire dataset is available next to

Nov 25

Emilia Manko, … Baby Anusha Satravada3

Nov 24

Access to HCMI dataset

Hi Emilia, Thank you for reaching out. Though the study is already available on cBioPortal, the

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Access to HCMI dataset

Hi Emilia, Thank you for reaching out. Though the study is already available on cBioPortal, the

Nov 24

Carlos Espinosa, Prasanna Jagannathan3

Nov 21

SAML metadata not found on new version 6.4.x

No, our institution has their own idp. El vie, 21 de nov de 2025, 6:34 am, Prasanna Jagannathan <

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SAML metadata not found on new version 6.4.x

No, our institution has their own idp. El vie, 21 de nov de 2025, 6:34 am, Prasanna Jagannathan <

Nov 21

Gerardo Ramirez Mejia, … Nikolaus Schultz5

Nov 20

Doubt about some samples

Dear Prasanna. Thanks a lot for your kindly response. The additional samples were observed using the

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Doubt about some samples

Dear Prasanna. Thanks a lot for your kindly response. The additional samples were observed using the

Nov 20

Shihab Dider, Ruslan Forostianov2

Nov 18

Constructing stable URLs documentation outdated?

Hi Shihab, I was not aware about the link. What you are explaining sounds like a bug. You might want

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Constructing stable URLs documentation outdated?

Hi Shihab, I was not aware about the link. What you are explaining sounds like a bug. You might want

Nov 18

Khonaw Klader, Guizela Huelsz Prince2

Nov 17

Hello! cBioPortal focuses mainly on somatic mutations, copy-number alterations, mRNA / protein

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Hello! cBioPortal focuses mainly on somatic mutations, copy-number alterations, mRNA / protein

Nov 17

Dario Dilernia, Nikolaus Schultz3

Nov 14

Help with querying data

Thank you, Niki. This is very helpful. I still need to explore the API but can that type of

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Help with querying data

Thank you, Niki. This is very helpful. I still need to explore the API but can that type of

Nov 14

Megan Harper, Aaron L3

Nov 13

Group Filtering Issues

Ok, I think we have an idea about the problem, though it may be difficult to fix unfortunately. There

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Group Filtering Issues

Ok, I think we have an idea about the problem, though it may be difficult to fix unfortunately. There

Nov 13

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