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cBioPortal for Cancer Genomics Discussion Group

1–30 of 5105

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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Ji Hen Lau, Priti Kumari2

Apr 18

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

Hi Ji Hen, Can you try adding Entrez ID in your data files (mutation and Copy number) and see if that

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

Hi Ji Hen, Can you try adding Entrez ID in your data files (mutation and Copy number) and see if that

Apr 18

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

Allen, Destiney X, Nikolaus Schultz2

Apr 18

Mutations tab annotations

Dear Destiney, OncoKB annotations are retrieved in real time from the OncoKB database, which itself

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Mutations tab annotations

Dear Destiney, OncoKB annotations are retrieved in real time from the OncoKB database, which itself

Apr 18

Harry Sun, de Bruijn, Ino8

Apr 17

Why did I use Maven build cbioportal v6.1.0,6.2.0,6.2.1 and get failed ?

Ino, cBioportal v6.2.1 doesn't work after I completed "mvn -DskipTests clean install"

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Why did I use Maven build cbioportal v6.1.0,6.2.0,6.2.1 and get failed ?

Ino, cBioportal v6.2.1 doesn't work after I completed "mvn -DskipTests clean install"

Apr 17

He, Siyi [JRDUS NON-J&J], Priti Kumari2

Apr 17

Question for cBioPortal data dictionary

Hi Siyi, You can find more information here: https://docs.cbioportal.org/file-formats/#mutation-data

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Question for cBioPortal data dictionary

Hi Siyi, You can find more information here: https://docs.cbioportal.org/file-formats/#mutation-data

Apr 17

Apr 17

cBioPortal Scavenger Hunt

Hello all! As a part of the rollout of the Fred Hutch instance of cBioPortal, we are planning a

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cBioPortal Scavenger Hunt

Hello all! As a part of the rollout of the Fred Hutch instance of cBioPortal, we are planning a

Apr 17

Juan Antonio Raygoza Garay

Apr 17

saml user email and name

Hi, i'm running cbioportal using docker and got saml to work, but the button on the top left show

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saml user email and name

Hi, i'm running cbioportal using docker and got saml to work, but the button on the top left show

Apr 17

Kiran, … Gaofei Zhao6

Apr 17

cBioPortal v6.0.24 : SAML integration not using existing authorities from the database

Hi Kiran, I believe we're still using the authorities table for access control (with authenticate

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cBioPortal v6.0.24 : SAML integration not using existing authorities from the database

Hi Kiran, I believe we're still using the authorities table for access control (with authenticate

Apr 17

Harika Gannu, Benjamin Gross6

Apr 17

cbioportal https

Hi Harika, I'm glad you are making progress. Someone from another post in the Google Group had a

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cbioportal https

Hi Harika, I'm glad you are making progress. Someone from another post in the Google Group had a

Apr 17

Akshaya Vs, Benjamin Gross2

Apr 14

Mutations across studies

Hi, According to documentation, get_mutations_by_study should return a data frame in MAF file format,

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Mutations across studies

Hi, According to documentation, get_mutations_by_study should return a data frame in MAF file format,

Apr 14

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

ROSANA XAVIER SOUZA, Prasanna Jagannathan3

Apr 9

Clarification Regarding the "Mutation Count" Variable in the Breast Invasive Carcinoma (TCGA, PanCancer Atlas) Study

Dear Jag, Thank you very much for your prompt and helpful response. Your explanation regarding the

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Clarification Regarding the "Mutation Count" Variable in the Breast Invasive Carcinoma (TCGA, PanCancer Atlas) Study

Dear Jag, Thank you very much for your prompt and helpful response. Your explanation regarding the

Apr 9

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

Vosmeijer, Ilse, Pieter Lukasse6

Apr 8

Display of oncoplot seems to have a bug

Thanks for the details. I tried a big oncoprint in Edge as well, but it looks fine on my side (see

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Display of oncoplot seems to have a bug

Thanks for the details. I tried a big oncoprint in Edge as well, but it looks fine on my side (see

Apr 8

Nisanur Güzel, cBioPortal for Cancer Genomics Discussion Group2

Apr 3

Inquiry Regarding cBioPortal Integration with R Studio

Hi Nisanur, Please refer to the cBioPortal documentation on how to use cBioPortal with R Studio. You

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Inquiry Regarding cBioPortal Integration with R Studio

Hi Nisanur, Please refer to the cBioPortal documentation on how to use cBioPortal with R Studio. You

Apr 3

Harika Gannu, … Zain-ul-Abideen Nasir5

Apr 3

compatible keycloak version for cbioportal version 6.0.24

Hi Harika, cBioPortal Docker Compose setup has been updated to use Keycloak v16 (https://github.com/

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compatible keycloak version for cbioportal version 6.0.24

Hi Harika, cBioPortal Docker Compose setup has been updated to use Keycloak v16 (https://github.com/

Apr 3

Bothe, Gerald W

Apr 3

Restrict a view to the C-terminus of a protein

Hi in the mutation view, eg https://www.cbioportal.org/results/mutations?case_set_id=

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Restrict a view to the C-terminus of a protein

Hi in the mutation view, eg https://www.cbioportal.org/results/mutations?case_set_id=

Apr 3

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

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

Andi L., Pieter Lukasse3

Mar 31

MSK-CHORD sampling surgery times

Hi Pieter, thank you very much for your help here. Indeed as your example shows, combining these two

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MSK-CHORD sampling surgery times

Hi Pieter, thank you very much for your help here. Indeed as your example shows, combining these two

Mar 31

Sistemisti Rete, Pieter Lukasse2

Mar 31

cBioPortal user reported error

Hi, Thanks for reporting. Is this still happening? Can you please point me to the right page where

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cBioPortal user reported error

Hi, Thanks for reporting. Is this still happening? Can you please point me to the right page where

Mar 31

bob, de Bruijn, Ino2

Mar 25

Questions from beginners about the AJCC pathologist T stage classification

Thanks for reaching out! Which study is this? It might be described in the accompanying article what

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Questions from beginners about the AJCC pathologist T stage classification

Thanks for reaching out! Which study is this? It might be described in the accompanying article what

Mar 25

Rye Visualization, Gaofei Zhao2

Mar 25

Error: "entityId cannot be null or empty" in cBioPortal SAML2 Integration with Keycloak

Hi Rye, If your cBioPortal version is greater than 6, you can refer to this documentation to set up

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Error: "entityId cannot be null or empty" in cBioPortal SAML2 Integration with Keycloak

Hi Rye, If your cBioPortal version is greater than 6, you can refer to this documentation to set up

Mar 25

Matthew Grimmer, de Bruijn, Ino2

Mar 25

MAF generation: Genome Nexus vs vcf2maf

Hi Matthew, Thanks for reaching out! The vcf2maf outputs work fine too. One thing to consider is that

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MAF generation: Genome Nexus vs vcf2maf

Hi Matthew, Thanks for reaching out! The vcf2maf outputs work fine too. One thing to consider is that

Mar 25

Akhil Wali, lisman...@gmail.com2

Mar 25

General Questions

Hi Akhil, For studies that do have expression data, it can be added to a query. To produce a query

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General Questions

Hi Akhil, For studies that do have expression data, it can be added to a query. To produce a query

Mar 25

Costello, Heather, … lisman...@gmail.com7

Mar 25

API query question

Hi Heather, it's unclear if this thread is resolved. Is there still an outstanding problem or can

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API query question

Hi Heather, it's unclear if this thread is resolved. Is there still an outstanding problem or can

Mar 25

Sriram Gubbi, … Curation Team5

Mar 24

Query regarding change in frequency of FLCN variants

Hi Sriram, Thank you for reaching out with your question regarding the changes in the FLCN oncoprint.

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Query regarding change in frequency of FLCN variants

Hi Sriram, Thank you for reaching out with your question regarding the changes in the FLCN oncoprint.

Mar 24

Joseph, Greg, … Pieter Lukasse8

Mar 24

Local cBioPortal instance - data question

Hi Ji Hen, How did this go? Best, Pieter On Wed, Feb 19, 2025 at 6:49 AM Ji Hen Lau <laujihen@

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Local cBioPortal instance - data question

Hi Ji Hen, How did this go? Best, Pieter On Wed, Feb 19, 2025 at 6:49 AM Ji Hen Lau <laujihen@

Mar 24

Waryszak Marcin, … Kiran28

Mar 21

Thank you Marcin for the reply. I am not using KeyCloak instead I am using our own SSO. I am using

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Thank you Marcin for the reply. I am not using KeyCloak instead I am using our own SSO. I am using

Mar 21

Dr. Avrajit Chakraborty, ole...@thehyve.nl3

Mar 20

problem_validateData.py

Dear Oleguer, Thanks for your response. I will try it and update further. Regards avrajit chakraborty

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problem_validateData.py

Dear Oleguer, Thanks for your response. I will try it and update further. Regards avrajit chakraborty

Mar 20

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