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cBioPortal for Cancer Genomics Discussion Group

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olofin daniel, Nikolaus Schultz2

Jun 24

Inquiry About Using cBioPortal Data for Publication

Dear Daniel, Thank you for your interest in using data from cBioPortal. There are no restrictions

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Inquiry About Using cBioPortal Data for Publication

Dear Daniel, Thank you for your interest in using data from cBioPortal. There are no restrictions

Jun 24

Bullen, Catherine (NIH/NCI) [C], Benjamin Gross4

Jun 18

Mutation Count discrepancy

Hi Catie, I've added Ramya Madupuri to this email. She is on our data curation team and will be

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Mutation Count discrepancy

Hi Catie, I've added Ramya Madupuri to this email. She is on our data curation team and will be

Jun 18

Hao-Kuen Lin, Benjamin Gross3

Jun 16

Question regarding data harmonizing

Thank you! On Mon, Jun 16, 2025 at 9:54 AM Benjamin Gross <benjami...@gmail.com> wrote: Hi

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Question regarding data harmonizing

Thank you! On Mon, Jun 16, 2025 at 9:54 AM Benjamin Gross <benjami...@gmail.com> wrote: Hi

Jun 16

Ji Hen Lau, Benjamin Gross3

Jun 15

Import patient without sample

Hi Benjamin, Thanks for the clarification ! Ji Hen On Saturday, 14 June 2025 at 00:04:16 UTC+8

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Import patient without sample

Hi Benjamin, Thanks for the clarification ! Ji Hen On Saturday, 14 June 2025 at 00:04:16 UTC+8

Jun 15

Qingzhi Liu, Pieter Lukasse2

Jun 2

Request for Clinical Information Website

Hi Qingzhi, Thanks for reporting. Can you please add some more information on where this is happening

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Request for Clinical Information Website

Hi Qingzhi, Thanks for reporting. Can you please add some more information on where this is happening

Jun 2

Guy Froyen, de Bruijn, Ino5

Jun 2

Hi Ino, It's a pity that the COSMIC column is no longer available in cBioPortal but I understand

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Hi Ino, It's a pity that the COSMIC column is no longer available in cBioPortal but I understand

Jun 2

Aharon Bensadoun, Pieter Lukasse2

Jun 2

Entra ID saml using Docker

Hi Aharon, Thanks for your question. I'm not sure if you already found the deployment docs? You

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Entra ID saml using Docker

Hi Aharon, Thanks for your question. I'm not sure if you already found the deployment docs? You

Jun 2

Igor Entin, de Bruijn, Ino2

Jun 6

Fw: Gene expression data with sensitivity scores

Hi Igor, Thanks for reaching out! From the homepage there is a link to filter by “data type”. You can

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Fw: Gene expression data with sensitivity scores

Hi Igor, Thanks for reaching out! From the homepage there is a link to filter by “data type”. You can

Jun 6

Strunilin, Ilya, Aaron L2

May 27

Hi Ilya, Please try again thanks, it should be resolved. --Aaron On Tue, May 27, 2025 at 7:25 AM

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Hi Ilya, Please try again thanks, it should be resolved. --Aaron On Tue, May 27, 2025 at 7:25 AM

May 27

Kinga Michalik, de Bruijn, Ino2

Jun 6

Functionalities

Hi Kinga, Thanks for reaching out! > 1. do the reverse selection? For now I can only select

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Functionalities

Hi Kinga, Thanks for reaching out! > 1. do the reverse selection? For now I can only select

Jun 6

Ana Clara Carrera, … de Bruijn, Ino12

Jun 6

cBioPortal user reported error

Hi Rachel, Do you still see this issue? Thanks! Ino From: cbiop...@googlegroups.com <cbioportal@

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cBioPortal user reported error

Hi Rachel, Do you still see this issue? Thanks! Ino From: cbiop...@googlegroups.com <cbioportal@

Jun 6

Andrea Aquino Cruz, Priti Kumari3

Apr 22

Request for TP53 Data

Hi Andrea, You can download all the data from the Datahub. Hope this helps, Priti On Tue, Apr 22,

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Request for TP53 Data

Hi Andrea, You can download all the data from the Datahub. Hope this helps, Priti On Tue, Apr 22,

Apr 22

彭仲特, Priti Kumari2

Apr 21

Hi zhongte, Source data for TCGA studies are available in the Genomic Data Commons. They also have

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Hi zhongte, Source data for TCGA studies are available in the Genomic Data Commons. They also have

Apr 21

Lucas Wang, Priti Kumari2

Apr 22

Hi Lucas, You can download all mutations from the Datahub. We do not keep information on the

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Hi Lucas, You can download all mutations from the Datahub. We do not keep information on the

Apr 22

Ji Hen Lau, Priti Kumari4

Apr 22

Issue with Discrete CNA Not Showing in Mutations Tab (CGHcall, sWGS)

Hi, I think I kind of sorted the issue out. It seems there's some internal data structure error

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Issue with Discrete CNA Not Showing in Mutations Tab (CGHcall, sWGS)

Hi, I think I kind of sorted the issue out. It seems there's some internal data structure error

Apr 22

Filliol, Aveline, de Bruijn, Ino2

Apr 11

Multiplex IF data deposition

Hi Aveline, Thanks so much for reaching out! We can def support visualization of multiplex IF data We

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Multiplex IF data deposition

Hi Aveline, Thanks so much for reaching out! We can def support visualization of multiplex IF data We

Apr 11

MOLONEY, Kate (SALISBURY NHS FOUNDATION TRUST), … Benjamin Gross6

Apr 18

GENIE data access

Ok, let me know if you run into any more issues logging in. -Benjamin On Apr 18, 2025, at 5:21 PM,

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GENIE data access

Ok, let me know if you run into any more issues logging in. -Benjamin On Apr 18, 2025, at 5:21 PM,

Apr 18

Soheil Shams, Prasanna Jagannathan3

Apr 9

downloading expression and mutation data

Dear Jag Thank you for the helpful reply. Best regards Soheil From: Prasanna Jagannathan <

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downloading expression and mutation data

Dear Jag Thank you for the helpful reply. Best regards Soheil From: Prasanna Jagannathan <

Apr 9

Md. Razib Khan, Pieter Lukasse3

Apr 1

Request for instructions for generating waterfall plot using cBioportal

Hi Razib, You are right, those steps are outdated. I have raised this issue as well. Just for the

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Request for instructions for generating waterfall plot using cBioportal

Hi Razib, You are right, those steps are outdated. I have raised this issue as well. Just for the

Apr 1

Zheng, Nianye, Ritika Kundra2

Apr 2

inquriry about impact data before 2016

Hi Nianye, I will move this to our internal MSK email to discuss this further. Thanks, Ritika On Thu,

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inquriry about impact data before 2016

Hi Nianye, I will move this to our internal MSK email to discuss this further. Thanks, Ritika On Thu,

Apr 2

Harika Gannu, … de Bruijn, Ino7

May 13

compatible keycloak version for cbioportal version 6.0.24

Hi Niels, Thanks for checking in – replied here: https://github.com/cBioPortal/cbioportal/issues/

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compatible keycloak version for cbioportal version 6.0.24

Hi Niels, Thanks for checking in – replied here: https://github.com/cBioPortal/cbioportal/issues/

May 13

内田士朗, Priti Kumari2

Feb 17

Inquiry Regarding Mutation Rate Calculation in cBioPortal’s Oncoprint

Hello Shiro, Is this using the public cBioPortal? Are you able to send the url to your query to

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Inquiry Regarding Mutation Rate Calculation in cBioPortal’s Oncoprint

Hello Shiro, Is this using the public cBioPortal? Are you able to send the url to your query to

Feb 17

Abubakr El Sobky, de Bruijn, Ino2

Feb 17

Google Summer of Code

Hi, Thanks for reaching out! We have applied for GSoC 2025 as a mentoring organization, but won't

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Google Summer of Code

Hi, Thanks for reaching out! We have applied for GSoC 2025 as a mentoring organization, but won't

Feb 17

Joseph Celidonio, Priti Kumari8

Feb 19

Hi Joe, It looks like there is a clinical field called "ICD10 classification" and based on

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Hi Joe, It looks like there is a clinical field called "ICD10 classification" and based on

Feb 19

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

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

Gupta, Princy, Pieter Lukasse2

Jan 23

Inquiry About GENIE Cohort v17.0 Appendix Cancer Dataset on cBioPortal

marking as duplicate of https://groups.google.com/g/cbioportal/c/ernVNdWFyKo On Wednesday, January 22

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Inquiry About GENIE Cohort v17.0 Appendix Cancer Dataset on cBioPortal

marking as duplicate of https://groups.google.com/g/cbioportal/c/ernVNdWFyKo On Wednesday, January 22

Jan 23

Jean Philippe Hugnot

Jan 10

Request for Guidance on Data Accessibility in cBioPortal

Dear BioPortal Team, I hope this message finds you well. I am reaching out regarding some WES data

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Request for Guidance on Data Accessibility in cBioPortal

Dear BioPortal Team, I hope this message finds you well. I am reaching out regarding some WES data

Jan 10

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

Prashanth Bachu, Karthik Kalletla2

12/16/24

Need Help in Setting up Keycloak Aunthentication to Cbioportal Using LDAP

Looks like a duplicate post. Please refer: https://groups.google.com/g/cbioportal/c/D0yVUP60F0I

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Need Help in Setting up Keycloak Aunthentication to Cbioportal Using LDAP

Looks like a duplicate post. Please refer: https://groups.google.com/g/cbioportal/c/D0yVUP60F0I

12/16/24

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