cBioPortal for Cancer Genomics Discussion Group

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Leila Kamkar, jagn...@gmail.com3

7:19 AM

Nginx proxy setting in Version6

Hi Jag, Many many thanks for your reply. I set the setting as you mentioned. But it still does not

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Nginx proxy setting in Version6

Hi Jag, Many many thanks for your reply. I set the setting as you mentioned. But it still does not

7:19 AM

Rafael Sainz, jagn...@gmail.com2

Dec 4

Need to query all studies -13 gene panel

Hi Rafael Sainz It is possible to create a virtual study combining all the studies of interest.

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Need to query all studies -13 gene panel

Hi Rafael Sainz It is possible to create a virtual study combining all the studies of interest.

Dec 4

Charles Olwal, jagn...@gmail.com2

Dec 4

Problems loading a study

Hi Charles, In the link below, all the parameters to the meta import script are given. https://docs.

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Problems loading a study

Hi Charles, In the link below, all the parameters to the meta import script are given. https://docs.

Dec 4

Andi L., Nikolaus Schultz5

Dec 4

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

Dec 4

Charles Olwal, Pieter Lukasse2

Dec 4

Hi Charles, Please see https://github.com/cBioPortal/cbioportal/blob/master/docs/Using-the-dataset-

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Hi Charles, Please see https://github.com/cBioPortal/cbioportal/blob/master/docs/Using-the-dataset-

Dec 4

Celine Kurniawan, Pieter Lukasse3

Dec 3

Clinvar annotation

Hi Pieter, Sorry for the late reply and not mentioning earlier that I used my own mutation data to

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Clinvar annotation

Hi Pieter, Sorry for the late reply and not mentioning earlier that I used my own mutation data to

Dec 3

SHI, YUFEI, Nikolaus Schultz2

Dec 2

RE: Aneuploidy Score

Apologies foe the delay. We have a ticket for this now and hope to get this done soon. In the

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RE: Aneuploidy Score

Apologies foe the delay. We have a ticket for this now and hope to get this done soon. In the

Dec 2

Alan Mackay, jagn...@gmail.com2

Dec 2

Submitting datasets to pedcBioPortal

Hi Alan, Congratulations on your publication. For cBioPortal.org, you can see the File format link so

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Submitting datasets to pedcBioPortal

Hi Alan, Congratulations on your publication. For cBioPortal.org, you can see the File format link so

Dec 2

J. N, jagn...@gmail.com4

Nov 29

What is "mixed" meaning in the patient CMS status?

Hi JN, The CMS is the Consensus Molecular Subtype from https://www.nature.com/articles/nm.3967. From

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What is "mixed" meaning in the patient CMS status?

Hi JN, The CMS is the Consensus Molecular Subtype from https://www.nature.com/articles/nm.3967. From

Nov 29

Jolien van Hooff, Ruslan Forostianov3

Nov 28

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

Nov 28

Monika Rosochowicz, Pieter Lukasse2

Nov 27

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

Nov 27

Thomas Pauli, Pieter Lukasse5

Nov 27

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

Nov 27

Ruslan Forostianov

Nov 26

Re: How to logout whit Microsoft

Hi Xinxin, Do you have access to the server logs? If so, it might be helpful to enable verbose

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Re: How to logout whit Microsoft

Hi Xinxin, Do you have access to the server logs? If so, it might be helpful to enable verbose

Nov 26

Ahmed Al Sharie, Aaron L5

Nov 25

Yea ----------------------------------------------------------------- Ahmed H. Al Sharie, MD PGY-1

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Yea ----------------------------------------------------------------- Ahmed H. Al Sharie, MD PGY-1

Nov 25

Niklas de Andrade Krätzig, Aaron L5

Nov 21

Overview grouping error: Unsuccessful HTTP response (mouse cbio)

Glad to hear it's fixed Niklas! On Thu, Nov 21, 2024 at 12:21 PM Niklas de Andrade Krätzig <

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Overview grouping error: Unsuccessful HTTP response (mouse cbio)

Glad to hear it's fixed Niklas! On Thu, Nov 21, 2024 at 12:21 PM Niklas de Andrade Krätzig <

Nov 21

xinxin chen, Ruslan Forostianov2

Nov 21

Import data with Docker has error

Hello Xinxin, Have you imported gene sets prior to importing the study_es_0 study? This study

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Import data with Docker has error

Hello Xinxin, Have you imported gene sets prior to importing the study_es_0 study? This study

Nov 21

Dr. Avrajit Chakraborty, de Bruijn, Ino3

Nov 21

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

Nov 21

Miranda Qing, … de Bruijn, Ino4

Nov 20

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:

Nov 20

MOHSEN SHEYKHHASAN, de Bruijn, Ino2

Nov 20

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

Nov 20

瑛, de Bruijn, Ino2

Nov 20

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

Nov 20

Hema Venugopal, … JJ Gao4

Nov 16

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

Nov 16

Efstathios Vlachavas, Zeynep Karagöz2

Nov 13

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

Nov 13

Mariana Gomes Da Silva Araujo, … JJ Gao6

Nov 13

Data discrepancies between API client and web portal - TCGA

Hello Nikki, Thank you again for the answer. I do not understand what you mean by “not shown in

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Data discrepancies between API client and web portal - TCGA

Hello Nikki, Thank you again for the answer. I do not understand what you mean by “not shown in

Nov 13

Brown, Miguel A, Yura Grabovska3

Nov 13

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

Nov 13

T Nishanth, Zeynep Karagöz3

Nov 13

deep sequencing

Hi T Nishanth, I would like to add to my previous reply that if you have used deep sequencing

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deep sequencing

Hi T Nishanth, I would like to add to my previous reply that if you have used deep sequencing

Nov 13

J. N, Jessica Singh2

Nov 13

How can I get 21 genes mutations situation and MSI, cancer sites from 5000 patients?

Hi Jiahui, Thank you for reaching out! Please let me know if you're working on a public

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How can I get 21 genes mutations situation and MSI, cancer sites from 5000 patients?

Hi Jiahui, Thank you for reaching out! Please let me know if you're working on a public

Nov 13

Charles Olwal, JJ Gao3

Nov 12

Problems loading datasets in local cbioportal

Hi Charles, Without looking at your data, it would be hard for us to figure out the issue. I can

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Problems loading datasets in local cbioportal

Hi Charles, Without looking at your data, it would be hard for us to figure out the issue. I can

Nov 12

Sanjana Sankar, Zeynep Karagöz3

Nov 10

CBio Portal- Correlation Analysis

Hi Ritika, Hope you are doing well! Just following up on my request regarding my single gene vs all

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CBio Portal- Correlation Analysis

Hi Ritika, Hope you are doing well! Just following up on my request regarding my single gene vs all

Nov 10

Maria, Gaofei Zhao3

Nov 8

docker compose up error Database not available yet (first time can take a few minutes to load seed database).

Hello Gaofei, Thank you for your response. I have checked all of these things and have installed

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docker compose up error Database not available yet (first time can take a few minutes to load seed database).

Hello Gaofei, Thank you for your response. I have checked all of these things and have installed

Nov 8

Joseph Celidonio, … Tali Mazor36

Nov 8

Variable Definition Confirmation

Hi Joe, There are a few ways you can do this, depending on exactly what you want. If you want samples

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Variable Definition Confirmation

Hi Joe, There are a few ways you can do this, depending on exactly what you want. If you want samples

Nov 8

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