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cBioPortal for Cancer Genomics Discussion Group

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Rachel Nelan, Prasanna Jagannathan2

Sep 25

CBioPortal 3D structure view issue

Hi Rachel Thanks for your email. Sorry for the inconvenience caused by 3D protein structure

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CBioPortal 3D structure view issue

Hi Rachel Thanks for your email. Sorry for the inconvenience caused by 3D protein structure

Sep 25

Sep 25

cancer type study

Hello, I've downloaded this data from cBioPortal as a test data: https://www.cbioportal.org/study

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cancer type study

Hello, I've downloaded this data from cBioPortal as a test data: https://www.cbioportal.org/study

Sep 25

Mehta, Nikita, Nikolaus Schultz3

Sep 24

Hi, Most of the somatic variant curation experts groups in ClinGen require knowing somatic status for

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Hi, Most of the somatic variant curation experts groups in ClinGen require knowing somatic status for

Sep 24

Ren, Danqing, Guizela Huelsz Prince4

Sep 24

RE: about data_mrna_seq_v2_rsem

Hi Dannie, The values in data_mrna_seq_v2_rsem are neither FPKM, nor FPKM-UQ, nor TPM. They are RSEM-

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RE: about data_mrna_seq_v2_rsem

Hi Dannie, The values in data_mrna_seq_v2_rsem are neither FPKM, nor FPKM-UQ, nor TPM. They are RSEM-

Sep 24

Waryszak Marcin, … frans frans6

Sep 23

OncoKB missing information

Hi Benjamin, In relation to your reply on " The default URL in code is https://public.api.oncokb

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OncoKB missing information

Hi Benjamin, In relation to your reply on " The default URL in code is https://public.api.oncokb

Sep 23

Margate Tristan, Guizela Huelsz Prince2

Sep 22

PFS status and meaning of progression

Hi Tristan, PFS_STATUS and PFS_MONTHS are columns that can be included in the clinical patient file;

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PFS status and meaning of progression

Hi Tristan, PFS_STATUS and PFS_MONTHS are columns that can be included in the clinical patient file;

Sep 22

Aaron Atkinson, Guizela Huelsz Prince2

Sep 22

Study example question

Hi Aaron, Are you maybe thinking about timeline files? These are files that contain longitudinal

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Study example question

Hi Aaron, Are you maybe thinking about timeline files? These are files that contain longitudinal

Sep 22

An-Ting Jhuang, Guizela Huelsz Prince3

Sep 22

MDS IWG 2022 dataset - ask for a data dictionary

Hi An-Ting Jhuang, The 397 samples refer to small TP53 mutations such as SNVs and INDELs, while the

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MDS IWG 2022 dataset - ask for a data dictionary

Hi An-Ting Jhuang, The 397 samples refer to small TP53 mutations such as SNVs and INDELs, while the

Sep 22

刘玉杰, Ruslan Forostianov2

Sep 22

Hello, Thank you for reporting the issue. I was not able to reproduce it though. Could you maybe give

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Hello, Thank you for reporting the issue. I was not able to reproduce it though. Could you maybe give

Sep 22

Truong,Danh Dinh, Ruslan Forostianov2

Sep 22

Links at the top

Hi Danh, Thank you for reporting the issue. I'll make sure it's reported on the issue board

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Links at the top

Hi Danh, Thank you for reporting the issue. I'll make sure it's reported on the issue board

Sep 22

Aslan, Deniz, Tim Kuijpers2

Sep 9

Download tsv problem help?

Dear Deniz, I believe you are running into the limitations of downloading large files via the browser

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Download tsv problem help?

Dear Deniz, I believe you are running into the limitations of downloading large files via the browser

Sep 9

frans frans, Tim Kuijpers3

Sep 9

merge multiple samples' or genes' mutations

Hi Tim, Thanks for the response! What I need is a mutation table (or something like an exportable tsv

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merge multiple samples' or genes' mutations

Hi Tim, Thanks for the response! What I need is a mutation table (or something like an exportable tsv

Sep 9

Kiran, Aaron L3

Sep 8

Out-of-date Version (Lodash)

Thank you, Aaron. I will deploy the pre-release and verify the application soon. thanks On Monday,

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Out-of-date Version (Lodash)

Thank you, Aaron. I will deploy the pre-release and verify the application soon. thanks On Monday,

Sep 8

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

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

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

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