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cBioPortal for Cancer Genomics Discussion Group

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Matthew Witek, Nikolaus Schultz2

12/9/25

Re: help with download

Hi Matthew, Unfortunately, that is not possible at the moment and is not a planned feature. I suggest

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Re: help with download

Hi Matthew, Unfortunately, that is not possible at the moment and is not a planned feature. I suggest

12/9/25

内田士朗, Prasanna Jagannathan2

11/25/25

Inquiry About Downloading “mRNA Expression Z-Score Relative to All Samples (log RNA-seq V2 RSEM)” for Breast Invasive Carcinoma (TCGA, PanCancer Atlas)

Hi Shiro Thanks for emailing the cBioPortal team. The link to the entire dataset is available next to

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Inquiry About Downloading “mRNA Expression Z-Score Relative to All Samples (log RNA-seq V2 RSEM)” for Breast Invasive Carcinoma (TCGA, PanCancer Atlas)

Hi Shiro Thanks for emailing the cBioPortal team. The link to the entire dataset is available next to

11/25/25

Costello, Heather, Ritika Kundra2

11/26/25

Pptc link heads-up

Hi Heather, Thanks for notifying us. The link has been updated. Ritika On Mon, Nov 24, 2025 at 4:07

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Pptc link heads-up

Hi Heather, Thanks for notifying us. The link has been updated. Ritika On Mon, Nov 24, 2025 at 4:07

11/26/25

Emilia Manko, … Anu Vijay5

Jan 26

Access to HCMI dataset

Hi Emilia, Hope you are doing well! Thank you for following up. At the moment, the associated paper

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Access to HCMI dataset

Hi Emilia, Hope you are doing well! Thank you for following up. At the moment, the associated paper

Jan 26

Gerardo Ramirez Mejia, … Nikolaus Schultz5

11/20/25

Doubt about some samples

Dear Prasanna. Thanks a lot for your kindly response. The additional samples were observed using the

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Doubt about some samples

Dear Prasanna. Thanks a lot for your kindly response. The additional samples were observed using the

11/20/25

Rory Johnson, Zeynep Karagöz3

11/4/25

can't see expression data for TCGA

Zeynep thanks so much for your helpful reply and excellent support! I'll check this out.

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can't see expression data for TCGA

Zeynep thanks so much for your helpful reply and excellent support! I'll check this out.

11/4/25

Jane Liang, Nikolaus Schultz2

10/22/25

Inquiry About Availability of VCF Files from MSG_CHORD

Hi Jingyun, The mutations data for the MSK-CHORD study (in MAF format) is available via the

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Inquiry About Availability of VCF Files from MSG_CHORD

Hi Jingyun, The mutations data for the MSK-CHORD study (in MAF format) is available via the

10/22/25

Mai, Nick, Benjamin Gross2

10/2/25

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, -

10/2/25

dan jin, Benjamin Gross5

10/3/25

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

10/3/25

Summer Henderson, … Benjamin Gross12

10/7/25

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,

10/7/25

olofin daniel, Nikolaus Schultz2

6/24/25

Inquiry About Using cBioPortal Data for Publication

Dear Daniel, Thank you for your interest in using data from cBioPortal. There are no restrictions

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Inquiry About Using cBioPortal Data for Publication

Dear Daniel, Thank you for your interest in using data from cBioPortal. There are no restrictions

6/24/25

Bullen, Catherine (NIH/NCI) [C], Benjamin Gross4

6/18/25

Mutation Count discrepancy

Hi Catie, I've added Ramya Madupuri to this email. She is on our data curation team and will be

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Mutation Count discrepancy

Hi Catie, I've added Ramya Madupuri to this email. She is on our data curation team and will be

6/18/25

Hao-Kuen Lin, Benjamin Gross3

6/16/25

Question regarding data harmonizing

Thank you! On Mon, Jun 16, 2025 at 9:54 AM Benjamin Gross <benjami...@gmail.com> wrote: Hi

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Question regarding data harmonizing

Thank you! On Mon, Jun 16, 2025 at 9:54 AM Benjamin Gross <benjami...@gmail.com> wrote: Hi

6/16/25

Ji Hen Lau, Benjamin Gross3

6/15/25

Import patient without sample

Hi Benjamin, Thanks for the clarification ! Ji Hen On Saturday, 14 June 2025 at 00:04:16 UTC+8

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Import patient without sample

Hi Benjamin, Thanks for the clarification ! Ji Hen On Saturday, 14 June 2025 at 00:04:16 UTC+8

6/15/25

Qingzhi Liu, Pieter Lukasse2

6/2/25

Request for Clinical Information Website

Hi Qingzhi, Thanks for reporting. Can you please add some more information on where this is happening

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Request for Clinical Information Website

Hi Qingzhi, Thanks for reporting. Can you please add some more information on where this is happening

6/2/25

Guy Froyen, de Bruijn, Ino5

6/2/25

Hi Ino, It's a pity that the COSMIC column is no longer available in cBioPortal but I understand

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Hi Ino, It's a pity that the COSMIC column is no longer available in cBioPortal but I understand

6/2/25

Aharon Bensadoun, Pieter Lukasse2

6/2/25

Entra ID saml using Docker

Hi Aharon, Thanks for your question. I'm not sure if you already found the deployment docs? You

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Entra ID saml using Docker

Hi Aharon, Thanks for your question. I'm not sure if you already found the deployment docs? You

6/2/25

Igor Entin, de Bruijn, Ino2

6/6/25

Fw: Gene expression data with sensitivity scores

Hi Igor, Thanks for reaching out! From the homepage there is a link to filter by “data type”. You can

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Fw: Gene expression data with sensitivity scores

Hi Igor, Thanks for reaching out! From the homepage there is a link to filter by “data type”. You can

6/6/25

Strunilin, Ilya, Aaron L2

5/27/25

Hi Ilya, Please try again thanks, it should be resolved. --Aaron On Tue, May 27, 2025 at 7:25 AM

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Hi Ilya, Please try again thanks, it should be resolved. --Aaron On Tue, May 27, 2025 at 7:25 AM

5/27/25

Kinga Michalik, de Bruijn, Ino2

6/6/25

Functionalities

Hi Kinga, Thanks for reaching out! > 1. do the reverse selection? For now I can only select

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Functionalities

Hi Kinga, Thanks for reaching out! > 1. do the reverse selection? For now I can only select

6/6/25

Ana Clara Carrera, … de Bruijn, Ino12

6/6/25

cBioPortal user reported error

Hi Rachel, Do you still see this issue? Thanks! Ino From: cbiop...@googlegroups.com <cbioportal@

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cBioPortal user reported error

Hi Rachel, Do you still see this issue? Thanks! Ino From: cbiop...@googlegroups.com <cbioportal@

6/6/25

Andrea Aquino Cruz, Priti Kumari3

4/22/25

Request for TP53 Data

Hi Andrea, You can download all the data from the Datahub. Hope this helps, Priti On Tue, Apr 22,

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Request for TP53 Data

Hi Andrea, You can download all the data from the Datahub. Hope this helps, Priti On Tue, Apr 22,

4/22/25

彭仲特, Priti Kumari2

4/21/25

Hi zhongte, Source data for TCGA studies are available in the Genomic Data Commons. They also have

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Hi zhongte, Source data for TCGA studies are available in the Genomic Data Commons. They also have

4/21/25

Lucas Wang, Priti Kumari2

4/22/25

Hi Lucas, You can download all mutations from the Datahub. We do not keep information on the

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Hi Lucas, You can download all mutations from the Datahub. We do not keep information on the

4/22/25

Ji Hen Lau, Priti Kumari4

4/22/25

Issue with Discrete CNA Not Showing in Mutations Tab (CGHcall, sWGS)

Hi, I think I kind of sorted the issue out. It seems there's some internal data structure error

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Issue with Discrete CNA Not Showing in Mutations Tab (CGHcall, sWGS)

Hi, I think I kind of sorted the issue out. It seems there's some internal data structure error

4/22/25

Filliol, Aveline, de Bruijn, Ino2

4/11/25

Multiplex IF data deposition

Hi Aveline, Thanks so much for reaching out! We can def support visualization of multiplex IF data We

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Multiplex IF data deposition

Hi Aveline, Thanks so much for reaching out! We can def support visualization of multiplex IF data We

4/11/25

MOLONEY, Kate (SALISBURY NHS FOUNDATION TRUST), … Benjamin Gross6

4/18/25

GENIE data access

Ok, let me know if you run into any more issues logging in. -Benjamin On Apr 18, 2025, at 5:21 PM,

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GENIE data access

Ok, let me know if you run into any more issues logging in. -Benjamin On Apr 18, 2025, at 5:21 PM,

4/18/25

Soheil Shams, Prasanna Jagannathan3

4/9/25

downloading expression and mutation data

Dear Jag Thank you for the helpful reply. Best regards Soheil From: Prasanna Jagannathan <

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downloading expression and mutation data

Dear Jag Thank you for the helpful reply. Best regards Soheil From: Prasanna Jagannathan <

4/9/25

Md. Razib Khan, Pieter Lukasse3

4/1/25

Request for instructions for generating waterfall plot using cBioportal

Hi Razib, You are right, those steps are outdated. I have raised this issue as well. Just for the

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Request for instructions for generating waterfall plot using cBioportal

Hi Razib, You are right, those steps are outdated. I have raised this issue as well. Just for the

4/1/25

Zheng, Nianye, Ritika Kundra2

4/2/25

inquriry about impact data before 2016

Hi Nianye, I will move this to our internal MSK email to discuss this further. Thanks, Ritika On Thu,

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inquriry about impact data before 2016

Hi Nianye, I will move this to our internal MSK email to discuss this further. Thanks, Ritika On Thu,

4/2/25

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