cBioPortal for Cancer Genomics Discussion Group

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Michael Rightmire, Ino de Bruijn5

4:15 PM

Clarifying data format, continuous copy number

Hi Michael, Apologies for the delay in replying. The negative integers can be safely ignored. They

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Clarifying data format, continuous copy number

Hi Michael, Apologies for the delay in replying. The negative integers can be safely ignored. They

4:15 PM

4:01 PM

cBioPortal Charts Question

Hello, I know that a user can create charts in the dashboard summary tab through selection of

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cBioPortal Charts Question

Hello, I know that a user can create charts in the dashboard summary tab through selection of

4:01 PM

SD, mram...@gmail.com2

2:12 PM

Issue downloading study tar from cBioPortalData R package

Hi Shruti, It seems like you are using the release version of cBioPortalData. It is meant to be

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Issue downloading study tar from cBioPortalData R package

Hi Shruti, It seems like you are using the release version of cBioPortalData. It is meant to be

2:12 PM

Alan Herbert, Ino de Bruijn2

12:41 PM

Hi Alan, Thanks for reaching out! We had some server issues this weekend. My apologies for the

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Hi Alan, Thanks for reaching out! We had some server issues this weekend. My apologies for the

12:41 PM

Lebow, Emily Schapira/Graduate Medical Education, Ino de Bruijn2

12:39 PM

Creating cbioportal account

Hi Emily, Thanks for reaching out! I replied in a separate email, let me know if you didn't get

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Creating cbioportal account

Hi Emily, Thanks for reaching out! I replied in a separate email, let me know if you didn't get

12:39 PM

Carlos Espinosa, Pim van Nierop2

Jul 30

Failed to build cbioportal

Dear Carlos, This error is caused by the host system unable to retrieve maven dependencies. What may

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Failed to build cbioportal

Dear Carlos, This error is caused by the host system unable to retrieve maven dependencies. What may

Jul 30

Kun-Lin Ho, … mram...@gmail.com4

Jul 29

questions about the c-bioportal api

Hi Kun-Lin Ho, I am the dev of the cBioPortalData R package. Ino reached out to me for assistance and

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questions about the c-bioportal api

Hi Kun-Lin Ho, I am the dev of the cBioPortalData R package. Ino reached out to me for assistance and

Jul 29

Kern, Kenneth A, … Sjoerd van Hagen6

Jul 29

Logging into cBIOPORTAL site

Hi Kenneth, Your colleague Won-Chul should be reaching out to you. I think he created your account

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Logging into cBIOPORTAL site

Hi Kenneth, Your colleague Won-Chul should be reaching out to you. I think he created your account

Jul 29

Seyma Bilgin, JJ Gao3

Jul 29

About GBM and Sample types

Hi Seyma, Sorry for the late reply. Would you please send me the URL of your query? Thanks, -JJ On

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About GBM and Sample types

Hi Seyma, Sorry for the late reply. Would you please send me the URL of your query? Thanks, -JJ On

Jul 29

Patricia Scott, … Ino de Bruijn3

Jul 29

question about definition of overall survival

Hi Patirica and Anna, Apologies for the delay in replying. Could you clarify which study you are

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question about definition of overall survival

Hi Patirica and Anna, Apologies for the delay in replying. Could you clarify which study you are

Jul 29

e...@clab.ventures, JJ Gao2

Jul 28

Dear Eva, I believe your colleague Sarolta Szőke have already got our permission to list cBioPortal:

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Dear Eva, I believe your colleague Sarolta Szőke have already got our permission to list cBioPortal:

Jul 28

Kathryn Kananen, … Aaron Lisman7

Jul 27

When comparing histology types there's a time out issue in portal

Hi guys, I'm happy to do a live debugging session on this. Should be able to tell pretty quick

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When comparing histology types there's a time out issue in portal

Hi guys, I'm happy to do a live debugging session on this. Should be able to tell pretty quick

Jul 27

Zachary Whitfield (WHITFIEZ), JJ Gao3

Jul 26

Large, single gene queries crash on Chrome, but not Firefox

Thank you so much for responding JJ. This was not on the public portal, but rather our own deployed

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Large, single gene queries crash on Chrome, but not Firefox

Thank you so much for responding JJ. This was not on the public portal, but rather our own deployed

Jul 26

Zhang, Christine, JJ Gao2

Jul 26

Question in combining different datasets for a given cancer type

Hi Christine, Yes, you can select multiple studies and then choose "Explore Selected Studies

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Question in combining different datasets for a given cancer type

Hi Christine, Yes, you can select multiple studies and then choose "Explore Selected Studies

Jul 26

Marc Deloger, John Reber9

Jul 23

"HTTP Status 500 – Internal Server Error" on public dataset "all_phase2_target_2018_pub"

Hi Marc, Sorry, wish I could be of more help. New to docker myself and I would think 'latest'

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"HTTP Status 500 – Internal Server Error" on public dataset "all_phase2_target_2018_pub"

Hi Marc, Sorry, wish I could be of more help. New to docker myself and I would think 'latest'

Jul 23

Santiago Enrique Sanchez, Ino de Bruijn2

Jul 23

Querying a large set of genes for mutual exclusivity

Hi Santiago, Thanks for reaching out! Sorry for the delay in replying cBioPortal's mututal

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Querying a large set of genes for mutual exclusivity

Hi Santiago, Thanks for reaching out! Sorry for the delay in replying cBioPortal's mututal

Jul 23

Jul 23

Question about OQL

Hi. I'm a new user of cbioportal. I used cbioportal to visualize the mutation landscape and I

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Question about OQL

Hi. I'm a new user of cbioportal. I used cbioportal to visualize the mutation landscape and I

Jul 23

Soriano Fernandez, Aroa, pr...@ds.dfci.harvard.edu2

Jul 22

Mistake notification from Aroa Soriano

Hi Aroa, Thank you for reporting this issue. We are working on a fix and will get back to your as

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Mistake notification from Aroa Soriano

Hi Aroa, Thank you for reporting this issue. We are working on a fix and will get back to your as

Jul 22

Anoop Sendamarai, Pim van Nierop5

Jul 16

Installation help

Hi Anoop, I suspect that you edited the portal.properties file on a windows computer thereby using

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Installation help

Hi Anoop, I suspect that you edited the portal.properties file on a windows computer thereby using

Jul 16

Mukherjee, Nabanita, Ino de Bruijn3

Jul 15

queries about conversion of raw data to log scale

Thank you so much Nabanita From: Ino de Bruijn <ino@ino.pm> Sent: Wednesday, July 14, 2021 10:

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queries about conversion of raw data to log scale

Thank you so much Nabanita From: Ino de Bruijn <ino@ino.pm> Sent: Wednesday, July 14, 2021 10:

Jul 15

Daniel Hurley, Pim van Nierop4

Jul 15

Recommended approach for restricting access to a prototype cBioPortal server

Hi Daniel, I think you still need to set up an external social IDP for it. cBioPortal supports Google

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Recommended approach for restricting access to a prototype cBioPortal server

Hi Daniel, I think you still need to set up an external social IDP for it. cBioPortal supports Google

Jul 15

Lucas Porras, … Nikolaus Schultz3

Jul 14

ESR1 Methylation data in breast cancer

Hi Lucas, Just a little additional detail: We pick one probe for each gene, based on correlation of

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ESR1 Methylation data in breast cancer

Hi Lucas, Just a little additional detail: We pick one probe for each gene, based on correlation of

Jul 14

Cyril Fournier, Aaron Lisman3

Jul 14

MutationMapper on local server

Hi Cyril, So, we could quite easily adapt the mutation mapper page (https://www.cbioportal.org/

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MutationMapper on local server

Hi Cyril, So, we could quite easily adapt the mutation mapper page (https://www.cbioportal.org/

Jul 14

Leylah Drusbosky, Ino de Bruijn2

Jul 13

Hosting cBioPortal locally

Hi Leylah, Thanks for reaching out! It is indeed possible to set up a local installation of

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Hosting cBioPortal locally

Hi Leylah, Thanks for reaching out! It is indeed possible to set up a local installation of

Jul 13

John Reber, Benjamin Gross36

Jul 13

Keycloak / SAML IDPSSODescriptor missing as an option

Yes, that was the fix. Thanks for all your help resolving this, John ------ John Reber Systems

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Keycloak / SAML IDPSSODescriptor missing as an option

Yes, that was the fix. Thanks for all your help resolving this, John ------ John Reber Systems

Jul 13

Thomas Pauli, Pim van Nierop3

Jul 9

cBioPortal Login error

Hi Pim, thank you very much for your response. I think I have correctly configured the email address

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cBioPortal Login error

Hi Pim, thank you very much for your response. I think I have correctly configured the email address

Jul 9

Katelyn Mullen, Benjamin Gross6

Jul 9

Mutations in PDAC datasets

Hi Katelyn, I'm sorry this fell through the cracks. As you probably know, within the cBioPortal

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Mutations in PDAC datasets

Hi Katelyn, I'm sorry this fell through the cracks. As you probably know, within the cBioPortal

Jul 9

James Reddoch, … Sjoerd van Hagen5

Jul 8

Question on cBioPortal

Re-sending to correct typo: On Jul 8, 2021, at 12:12 PM, James Reddoch <jimreddoch@gmail.com>

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Question on cBioPortal

Re-sending to correct typo: On Jul 8, 2021, at 12:12 PM, James Reddoch <jimreddoch@gmail.com>

Jul 8

Marc Deloger, Pim van Nierop3

Jul 6

Error when doing a gene query

Hi Marc, The problem here is that cBioPortal does not handle the files related to 'normal'

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Error when doing a gene query

Hi Marc, The problem here is that cBioPortal does not handle the files related to 'normal'

Jul 6

Kartika.V...@syngeneintl.com, Paul van Dijk2

Jul 5

Difficulties in downloading the data

Dear Kartika, Thanks for reaching out. Could you please be more specific? There are several places

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Difficulties in downloading the data

Dear Kartika, Thanks for reaching out. Could you please be more specific? There are several places

Jul 5

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