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cBioPortal for Cancer Genomics Discussion Group

1–30 of 5089

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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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

Leila Kamkar, … Benjamin Gross5

12/6/24

Nginx proxy setting in Version6

Many thanks, Benjamin. Yes, that is correct. The problem is fixed by setting this in application.

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Nginx proxy setting in Version6

Many thanks, Benjamin. Yes, that is correct. The problem is fixed by setting this in application.

12/6/24

Andi L., Nikolaus Schultz5

12/4/24

MSK-CHORD pre-entry treatment

Thanks again, for now everything is clear! Nikolaus Schultz schrieb am Montag, 2. Dezember 2024 um 17

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MSK-CHORD pre-entry treatment

Thanks again, for now everything is clear! Nikolaus Schultz schrieb am Montag, 2. Dezember 2024 um 17

12/4/24

Monika Rosochowicz, Pieter Lukasse2

11/27/24

Trouble getting data from the BRCA TCGA PanAtlas cBioPortal study

Hi Monika, I checked the same UI and it seems you have found a bug. Thanks for reporting! I've

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Trouble getting data from the BRCA TCGA PanAtlas cBioPortal study

Hi Monika, I checked the same UI and it seems you have found a bug. Thanks for reporting! I've

11/27/24

Thomas Pauli, Pieter Lukasse5

11/27/24

display namespaces in CNV and SV table per default

Fantastic! Thanks for confirming the solution of removing quotes works :) Best, Pieter PS: If you

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display namespaces in CNV and SV table per default

Fantastic! Thanks for confirming the solution of removing quotes works :) Best, Pieter PS: If you

11/27/24

Jolien van Hooff, Ruslan Forostianov3

11/28/24

Discrepancy mutations data file and patient view/clinical data

Hi, This makes a lot of sense, thank you! Best wishes, Jolien On Wednesday, November 27, 2024 at 3:15

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Discrepancy mutations data file and patient view/clinical data

Hi, This makes a lot of sense, thank you! Best wishes, Jolien On Wednesday, November 27, 2024 at 3:15

11/28/24

瑛, de Bruijn, Ino2

11/20/24

Hi, Thanks for sharing the error with us! The link currently seems to work. Could you share the steps

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Hi, Thanks for sharing the error with us! The link currently seems to work. Could you share the steps

11/20/24

MOHSEN SHEYKHHASAN, de Bruijn, Ino2

11/20/24

Inquiry About Protein Expression Data on cBioPortal

Hi Mohsen, Thanks for reaching out! For protein expression there is RPPA and Protein Mass Spec (see

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Inquiry About Protein Expression Data on cBioPortal

Hi Mohsen, Thanks for reaching out! For protein expression there is RPPA and Protein Mass Spec (see

11/20/24

Dr. Avrajit Chakraborty, de Bruijn, Ino3

11/21/24

which Annotatio tool _oncoprint

Hi Ino, Thanks for your mail. I understand the point you highlighted. Regards On Wed, Nov 20, 2024 at

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which Annotatio tool _oncoprint

Hi Ino, Thanks for your mail. I understand the point you highlighted. Regards On Wed, Nov 20, 2024 at

11/21/24

Efstathios Vlachavas, Zeynep Karagöz2

11/13/24

License terms and putative commercial usage of downloading specific gene-sets signatures through the cBioPortal web portal

Hi Efstathios, Thanks for reaching out to us! The gene lists available at the query view can be found

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License terms and putative commercial usage of downloading specific gene-sets signatures through the cBioPortal web portal

Hi Efstathios, Thanks for reaching out to us! The gene lists available at the query view can be found

11/13/24

Miranda Qing, … de Bruijn, Ino4

11/20/24

cBioPortal user reported error

Thanks Olivia! Could you describe the steps that led you to this error? Thanks so much! Ino From:

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cBioPortal user reported error

Thanks Olivia! Could you describe the steps that led you to this error? Thanks so much! Ino From:

11/20/24

Hema Venugopal, … JJ Gao4

11/16/24

Question about open PBTA database

Dear Zeynep and JianJiong, Thank you so much for your swift help! I will approach the authors of the

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Question about open PBTA database

Dear Zeynep and JianJiong, Thank you so much for your swift help! I will approach the authors of the

11/16/24

Brown, Miguel A, Yura Grabovska3

11/13/24

Re: [External]Chasing status of a study dataset

Hi Miguel, Thank you for getting back and for taking a look. It isn't the 2017 one unfortunately

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Re: [External]Chasing status of a study dataset

Hi Miguel, Thank you for getting back and for taking a look. It isn't the 2017 one unfortunately

11/13/24

10/11/24

download the mRNA z scores (RAW DATA)

Arushi Rai <rai...@udayton.edu>Hello, I have these four sample patient IDs that I extracted

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download the mRNA z scores (RAW DATA)

Arushi Rai <rai...@udayton.edu>Hello, I have these four sample patient IDs that I extracted

10/11/24

Waki Hosoda, Tali Mazor3

9/4/24

Error report_Oncoprinter

Hi Tali, Thank you so much for your advice. It worked again! Best regards, Waki From: Tali Mazor <

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Error report_Oncoprinter

Hi Tali, Thank you so much for your advice. It worked again! Best regards, Waki From: Tali Mazor <

9/4/24

Ariella Hanker, Tali Mazor3

8/29/24

cBioPortal Oncoprint problem

That worked, thank you! Ariella From: Tali Mazor <tma...@ds.dfci.harvard.edu> Sent: Thursday,

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cBioPortal Oncoprint problem

That worked, thank you! Ariella From: Tali Mazor <tma...@ds.dfci.harvard.edu> Sent: Thursday,

8/29/24

SARA GIL BERNABE, Tim Kuijpers2

8/29/24

Dear Sara, This is an error introduced in Chromium but has been resolved as of today. If you are

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Dear Sara, This is an error introduced in Chromium but has been resolved as of today. If you are

8/29/24

SARA GIL BERNABE, Aaron L3

8/29/24

CBIOPORTAL DID NOT DISPLAY ONCOPRINTER

Thank you Aaron! Sara Gil Bernabé Investigadora Predoctoral Patobiología del Cáncer Departamento de

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CBIOPORTAL DID NOT DISPLAY ONCOPRINTER

Thank you Aaron! Sara Gil Bernabé Investigadora Predoctoral Patobiología del Cáncer Departamento de

8/29/24

Lisa Eli, Tali Mazor2

8/29/24

help with error in oncoprinter

Hi Lisa, This is likely due to a bug in a recent version of Chromium. If you are using Google Chrome

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help with error in oncoprinter

Hi Lisa, This is likely due to a bug in a recent version of Chromium. If you are using Google Chrome

8/29/24

Siyun Lee, … Tali Mazor4

8/29/24

cBioPortal Oncoprinter Rendering Issue

Hello Tali, Thank you for the help! Working on another browser (Safari) worked. Sincerely, Siyun Lee

unread,

cBioPortal Oncoprinter Rendering Issue

Hello Tali, Thank you for the help! Working on another browser (Safari) worked. Sincerely, Siyun Lee

8/29/24

Erfan Heidari, Tali Mazor2

8/29/24

Request for Extended Access for Multiple Gene Query Submissions

Hi Erfan, Thanks for reaching out. Large queries are a challenge for our servers, so we have limited

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Request for Extended Access for Multiple Gene Query Submissions

Hi Erfan, Thanks for reaching out. Large queries are a challenge for our servers, so we have limited

8/29/24

Reem Bsoul, Tali Mazor2

8/29/24

Hi Reem, Different studies may define outcomes like disease-specific survival in different ways. Your

unread,

Hi Reem, Different studies may define outcomes like disease-specific survival in different ways. Your

8/29/24

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