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cBioPortal for Cancer Genomics Discussion Group

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Oct 15

Study Sample Question

Hello everyone, I have a question about a study sample. I have a group of patients with a particular

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Study Sample Question

Hello everyone, I have a question about a study sample. I have a group of patients with a particular

Oct 15

Laura Parrilla Monge, Nikolaus Schultz2

Oct 14

Create a Group from a User-Defined List

Hi Laura, You can add a gene specific chart in the study view via the “Charts” button on the top

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Create a Group from a User-Defined List

Hi Laura, You can add a gene specific chart in the study view via the “Charts” button on the top

Oct 14

Joanna Michelle Aniago, Nikolaus Schultz2

Oct 14

Failure in retrieval of requested information

Hi Joanna, I was able to run your query without any issues - can you please try again to see if the

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Failure in retrieval of requested information

Hi Joanna, I was able to run your query without any issues - can you please try again to see if the

Oct 14

Rebecca Sansale, … Aaron L5

Oct 14

Large Study Organization

thank you so much for this info! i will definitely try using the Clickhouse option, that seems

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Large Study Organization

thank you so much for this info! i will definitely try using the Clickhouse option, that seems

Oct 14

Samuel Kellen, … Benjamin Gross8

Oct 7

Unable to iniitalize cBioPortal off Docker

Hi Jason, The steps you are running are all you should need to do. Based on the provided snippet it

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Unable to iniitalize cBioPortal off Docker

Hi Jason, The steps you are running are all you should need to do. Based on the provided snippet it

Oct 7

Yi Q, Ritika Kundra2

Oct 7

Discrepancy in sample size and mutation frequencies V18

Hi Yi, Thank you for reaching out. For your first question, the total sequenced sample count is

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Discrepancy in sample size and mutation frequencies V18

Hi Yi, Thank you for reaching out. For your first question, the total sequenced sample count is

Oct 7

Summer Henderson, … Benjamin Gross12

Oct 7

queries regarding data sets

Thank you Benjamin, Do you know how we find which group it is in order to reach out? Thank you,

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queries regarding data sets

Thank you Benjamin, Do you know how we find which group it is in order to reach out? Thank you,

Oct 7

Waryszak Marcin, … Benjamin Gross7

Oct 6

OncoKB missing information

HI Frans, Thanks for your patience. My guess is public.api.oncokb.org is being used by the public

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OncoKB missing information

HI Frans, Thanks for your patience. My guess is public.api.oncokb.org is being used by the public

Oct 6

dan jin, Benjamin Gross5

Oct 3

mRNA expression, RSEM( Batch normalized from illumina Hiseq_RNAseq)

Thank you Benjamin! I will wait to see if anyone else in the group could provide some advice. Best

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mRNA expression, RSEM( Batch normalized from illumina Hiseq_RNAseq)

Thank you Benjamin! I will wait to see if anyone else in the group could provide some advice. Best

Oct 3

Aaron Atkinson, Guizela Huelsz Prince4

Oct 3

Study example question

Hi Aaron, I am not aware of any current functionality to handle two separate patient files. In fact,

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Study example question

Hi Aaron, I am not aware of any current functionality to handle two separate patient files. In fact,

Oct 3

Mai, Nick, Benjamin Gross2

Oct 2

Dataset Upload for Cancer Discovery Submission

Hi Nick, Please send an email to cdsi [at] mskcc.org and we can help you with this request. Best, -

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Dataset Upload for Cancer Discovery Submission

Hi Nick, Please send an email to cdsi [at] mskcc.org and we can help you with this request. Best, -

Oct 2

Setlem, Rohit, M.S., Prasanna Jagannathan2

Oct 1

Question on configuring default columns in cBioPortal

Hi Rohit, Thanks for the email. Currently the option is to display only default columns. However if

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Question on configuring default columns in cBioPortal

Hi Rohit, Thanks for the email. Currently the option is to display only default columns. However if

Oct 1

Xiaoyong Fu, Prasanna Jagannathan2

Sep 30

Encountered error in cBioPortal

Hi Xiaoyong Thanks for the email. I tried to reproduce the error at different times. But I was not

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Encountered error in cBioPortal

Hi Xiaoyong Thanks for the email. I tried to reproduce the error at different times. But I was not

Sep 30

Alain Pacis, Prasanna Jagannathan4

Sep 30

cancer type study

Hi Alain By default, the install process will import all the cancer types into type_of_cancer table.

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cancer type study

Hi Alain By default, the install process will import all the cancer types into type_of_cancer table.

Sep 30

jules, Prasanna Jagannathan2

Sep 29

cBioPortal user reported error

Hi Jules Thanks for emailing us. I was not able to reproduce this error using the URL that you shared

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cBioPortal user reported error

Hi Jules Thanks for emailing us. I was not able to reproduce this error using the URL that you shared

Sep 29

Florian Andersch, Prasanna Jagannathan2

Sep 29

Question about Gastric Cancer (OncoSG, 2018) dataset in cBioPortal

Hi Florian Thanks for your email. The issue is present in the underlying dataset files of the study.

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Question about Gastric Cancer (OncoSG, 2018) dataset in cBioPortal

Hi Florian Thanks for your email. The issue is present in the underlying dataset files of the study.

Sep 29

Truong,Danh Dinh, … Miguel Brown3

Sep 26

Links at the top

Hi Danh, Just a quick update. We have updated the links at the top to the best of our ability. We

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Links at the top

Hi Danh, Just a quick update. We have updated the links at the top to the best of our ability. We

Sep 26

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

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

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

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

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

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