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cBioPortal for Cancer Genomics Discussion Group

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10:38 AM

MDS IWG 2022 dataset - ask for a data dictionary

Hi, I'm a data scientist in RefinedScience and doing MDS-related research. I recently found your

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MDS IWG 2022 dataset - ask for a data dictionary

Hi, I'm a data scientist in RefinedScience and doing MDS-related research. I recently found your

10:38 AM

Juan Antonio Raygoza Garay, Gaofei Zhao3

Aug 29

Multiple docker instances

Hi Juan, Before diving into the technical details, I'd like to better understand your goals.

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Multiple docker instances

Hi Juan, Before diving into the technical details, I'd like to better understand your goals.

Aug 29

Lihui Yin, JJ Gao2

Aug 22

Sources of the Custom Driver annotations

Hi Lihui, Thank you so much for sharing! 🙂 -JJ On Fri, Aug 22, 2025 at 10:24 AM Lihui Yin <lihui.

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Sources of the Custom Driver annotations

Hi Lihui, Thank you so much for sharing! 🙂 -JJ On Fri, Aug 22, 2025 at 10:24 AM Lihui Yin <lihui.

Aug 22

Rodrigo Henrique Ramos, JJ Gao3

Aug 21

Inquiry on MAF-style mutation data for healthy individuals

Dear Gao, This is precisely what I need. Thank you very much. I am currently studying causal model

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Inquiry on MAF-style mutation data for healthy individuals

Dear Gao, This is precisely what I need. Thank you very much. I am currently studying causal model

Aug 21

Hakim, Sydney, JJ Gao3

Aug 21

OncoPrinter Question

Thank you! That is very helpful!! Sydney Hakim | Research Services Entry Professional | Hayashi

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OncoPrinter Question

Thank you! That is very helpful!! Sydney Hakim | Research Services Entry Professional | Hayashi

Aug 21

Jasmine Martinez, Nikolaus Schultz2

Aug 19

Dear Jasmine, Can you please confirm that the error you have observed is still there? I am able to

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Dear Jasmine, Can you please confirm that the error you have observed is still there? I am able to

Aug 19

tooearly, Nikolaus Schultz2

Aug 19

kindly request a revision of the clinical information codes

Dear Chang, Thank you for reaching out to us. I have cc'd Ritika, who leads our curation team.

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kindly request a revision of the clinical information codes

Dear Chang, Thank you for reaching out to us. I have cc'd Ritika, who leads our curation team.

Aug 19

Lila Taylor, … Tram Tran46

Aug 15

cBioPortal user reported error

Hi Benjamin, I was graphing the correlation of expression of 2 genes. In first crash, the graph was

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cBioPortal user reported error

Hi Benjamin, I was graphing the correlation of expression of 2 genes. In first crash, the graph was

Aug 15

Aug 14

Out-of-date Version (Lodash)

Hello there, We are using the cBioPortal version 6.2.0 and found a captioned vulnerability. Do you

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Out-of-date Version (Lodash)

Hello there, We are using the cBioPortal version 6.2.0 and found a captioned vulnerability. Do you

Aug 14

Summer Henderson, Benjamin Gross4

Aug 14

queries regarding data sets

Hi Summer, log-transformed z-scores are computed for each sample/gene against the average expression

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queries regarding data sets

Hi Summer, log-transformed z-scores are computed for each sample/gene against the average expression

Aug 14

Xiaodong Pang, Benjamin Gross3

Aug 12

Inquiry About Metadata Harmonization in cBioPortal

Dear Benjamin and Ritika, Thank you for your prompt response—I'm delighted to connect and learn

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Inquiry About Metadata Harmonization in cBioPortal

Dear Benjamin and Ritika, Thank you for your prompt response—I'm delighted to connect and learn

Aug 12

Waryszak Marcin, … Benjamin Gross5

Aug 12

OncoKB missing information

Hi John, The endpoint is /annotate/mutations/byProteinChange. The default URL in code is https://

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OncoKB missing information

Hi John, The endpoint is /annotate/mutations/byProteinChange. The default URL in code is https://

Aug 12

RAINFORD, Jethro (CAMBRIDGE UNIVERSITY HOSPITALS NHS FOUNDATION TRUST), Benjamin Gross2

Aug 8

Programatically downloading mutation data in tsv format

Hi Jethro, If you register with the AACR Project GENIE Public project on synapse, you should be able

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Programatically downloading mutation data in tsv format

Hi Jethro, If you register with the AACR Project GENIE Public project on synapse, you should be able

Aug 8

Jerry Zak, de Bruijn, Ino3

Aug 7

cBioportal down?

OK, thanks! It works on my home network now. I will reach out if there are any issues. Best, Jerry

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cBioportal down?

OK, thanks! It works on my home network now. I will reach out if there are any issues. Best, Jerry

Aug 7

Emily Jude - SVHNS, de Bruijn, Ino2

Aug 7

Hi Emily, Thanks for letting us know! We had some server outage– should be working now, let us know

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Hi Emily, Thanks for letting us know! We had some server outage– should be working now, let us know

Aug 7

Juan Antonio Raygoza Garay, … JJ Gao6

Aug 6

Hide Clinical data tab

Hi Juan, I've created a ticket on this: https://github.com/cBioPortal/cbioportal/issues/11653. It

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Hide Clinical data tab

Hi Juan, I've created a ticket on this: https://github.com/cBioPortal/cbioportal/issues/11653. It

Aug 6

Mahapatra, Somnath, Prasanna Jagannathan2

Aug 6

Failed analysis

Hi Somnath Thanks for emailing cBioPortal. I am able to reproduce the error. Can you share the

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Failed analysis

Hi Somnath Thanks for emailing cBioPortal. I am able to reproduce the error. Can you share the

Aug 6

Sachin Kumar, Prasanna Jagannathan2

Aug 5

RNASeq data correlation

Hi Sachin Please checkout our FAQ on RNA data. https://docs.cbioportal.org/user-guide/faq/#rna thanks

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RNASeq data correlation

Hi Sachin Please checkout our FAQ on RNA data. https://docs.cbioportal.org/user-guide/faq/#rna thanks

Aug 5

ROCCA ANDREA, Ramya Madupuri5

Jul 31

Different results from pathway table

Dear Ramya thank you very much for your assistance. I will obviously keep the last result. Perhaps,

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Different results from pathway table

Dear Ramya thank you very much for your assistance. I will obviously keep the last result. Perhaps,

Jul 31

Suganya MS, Prasanna Jagannathan2

Jul 31

SSL certificate error

Hi Suganya Can you check if the study got imported successfully when OKTA is disabled? The study page

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SSL certificate error

Hi Suganya Can you check if the study got imported successfully when OKTA is disabled? The study page

Jul 31

Adam Clayton, Prasanna Jagannathan2

Jul 30

Potential discrepancy with RPS15 NM_001018

Hi Adam Can you provide an example or link to the page where the difference occurs? thanks Jag On Wed

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Potential discrepancy with RPS15 NM_001018

Hi Adam Can you provide an example or link to the page where the difference occurs? thanks Jag On Wed

Jul 30

Cristina Camps Fajol, JJ Gao2

Jul 30

cbioportal synthetic lethality

Hi Cristina, Thank you for reaching out to us. Apologies for the late reply. Our tutorials are

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cbioportal synthetic lethality

Hi Cristina, Thank you for reaching out to us. Apologies for the late reply. Our tutorials are

Jul 30

Adam Clayton, … Aaron L3

Jul 30

cbioportal 503 Service temporarily unavailable

not planned. looks to be back up. we'll look into outage thanks On Wed, Jul 30, 2025 at 9:53 AM

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cbioportal 503 Service temporarily unavailable

not planned. looks to be back up. we'll look into outage thanks On Wed, Jul 30, 2025 at 9:53 AM

Jul 30

Stephen Rocca, Pieter Lukasse3

Jul 29

44 Y chromosome genes found in breast cancer cell line AU-565

Hi Pieter, Thanks very much. That actually makes sense. I appreciate your help. Sincerely, Steve

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44 Y chromosome genes found in breast cancer cell line AU-565

Hi Pieter, Thanks very much. That actually makes sense. I appreciate your help. Sincerely, Steve

Jul 29

Hoda Naseri, Ramya Madupuri2

Jul 29

Request for CT Imaging Data - TCGA-UCEC (PanCancer Atlas)

Hi Hoda, Thanks for reaching out. The CT scans from TCGA are publicly available on the IDC Portal. To

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Request for CT Imaging Data - TCGA-UCEC (PanCancer Atlas)

Hi Hoda, Thanks for reaching out. The CT scans from TCGA are publicly available on the IDC Portal. To

Jul 29

Marc Rijksen, Pieter Lukasse2

Jul 29

Onco Query Language (OQL) AND Operator and conditional gene groups

Hi Marc, Thanks for the questions. I don't think OQL supports AND at this moment. But you can run

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Onco Query Language (OQL) AND Operator and conditional gene groups

Hi Marc, Thanks for the questions. I don't think OQL supports AND at this moment. But you can run

Jul 29

Jane Kim, JJ Gao3

Jul 29

cBioPortal retrieval error

Thank you for your help, JJ! ********************** Jane C. Kim, Ph.D. Associate Professor, Faculty

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cBioPortal retrieval error

Thank you for your help, JJ! ********************** Jane C. Kim, Ph.D. Associate Professor, Faculty

Jul 29

Bauche, David, JJ Gao3

Jul 29

Error when performing a quick search

Hi JJ, It works now! Thank you, David From: JJ Gao <jianji...@gmail.com> Sent: Monday, July

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Error when performing a quick search

Hi JJ, It works now! Thank you, David From: JJ Gao <jianji...@gmail.com> Sent: Monday, July

Jul 29

Jiali Pang, JJ Gao2

Jul 28

MutationMapper is temporally down?

Thank you for reporting this to us. We have experienced some website issue today and it has been

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MutationMapper is temporally down?

Thank you for reporting this to us. We have experienced some website issue today and it has been

Jul 28

Terran Stenger, JJ Gao2

Jul 28

Issue with Charts

Thank you for reporting this to us. We have experienced some website issue today and it has been

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Issue with Charts

Thank you for reporting this to us. We have experienced some website issue today and it has been

Jul 28

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