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cBioPortal for Cancer Genomics Discussion Group

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Sachi Bhalchandra Tengse, Tali Mazor2

Jul 8

Error on CBioPortal

Hi Sachi, Thanks for reaching out. Can you please try again? We were having some issues with the site

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Error on CBioPortal

Hi Sachi, Thanks for reaching out. Can you please try again? We were having some issues with the site

Jul 8

Ng, Yuen-Keng, Tali Mazor2

Jul 8

cbioportal access error

Hi Yuen-Keng, Thanks for reaching out. Can you please try again? We were having some issues with the

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cbioportal access error

Hi Yuen-Keng, Thanks for reaching out. Can you please try again? We were having some issues with the

Jul 8

amsa...@mskcc.org

Jul 8

Start_TIME Field in Timeline Data

Hi, I'm looking at the CDSI timeline data for diagnosis events and trying to understand what the

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Start_TIME Field in Timeline Data

Hi, I'm looking at the CDSI timeline data for diagnosis events and trying to understand what the

Jul 8

阿力米热, Ritika Kundra2

Jul 8

API Access Issue for Public Dataset "bladder_msk_2025" from Published Study

Hello Alimire, The study is currently not in the portal. We are working with the authors to finalize

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API Access Issue for Public Dataset "bladder_msk_2025" from Published Study

Hello Alimire, The study is currently not in the portal. We are working with the authors to finalize

Jul 8

Anish Bhaswanth, … Ram RS9

Jul 7

hg38 for segmentation

Sorry to necro this post, but I'm in the exact situation as Anish - all my omics analyses use

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hg38 for segmentation

Sorry to necro this post, but I'm in the exact situation as Anish - all my omics analyses use

Jul 7

Cristina Camps Fajol

Jul 7

cbioportal synthetic lethality

Good morning, I'm Cristina Camps, postdoctoral researcher at the IR Sant Pau in Barcelona. I'

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cbioportal synthetic lethality

Good morning, I'm Cristina Camps, postdoctoral researcher at the IR Sant Pau in Barcelona. I'

Jul 7

Sandra Vergara, Aaron L2

Jul 2

cBioPortal Error

Sandra, can you try using another browser and see if the same thing happens? What browser/version are

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cBioPortal Error

Sandra, can you try using another browser and see if the same thing happens? What browser/version are

Jul 2

Bullen, Catherine (NIH/NCI) [C], de Bruijn, Ino3

Jul 2

Discrete CNA Table

Hi Ino, Thanks so much for the help. I loaded in both example TCGA studies (hg19 and hg38) as

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Discrete CNA Table

Hi Ino, Thanks so much for the help. I loaded in both example TCGA studies (hg19 and hg38) as

Jul 2

Jul 2

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

Hello, I'm studying common gene copy number alterations found in 4 cell lines that are sensitive

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

Hello, I'm studying common gene copy number alterations found in 4 cell lines that are sensitive

Jul 2

Emily Jude - SVHNS, JJ Gao3

Jul 2

Error accessing cbioportal today

Yep it started working again about an hour after that, so all good for the moment. Thanks, Emily From

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Error accessing cbioportal today

Yep it started working again about an hour after that, so all good for the moment. Thanks, Emily From

Jul 2

Melek Büyükgök, JJ Gao2

Jun 30

Inquiry Regarding Gleason Score and Histomorphology Data in TCGA Prostate Adenocarcinoma (PanCancer Atlas)

Hi Melek, Thanks for contacting us. One way to identity such data is to 1. open all prostate cancer

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Inquiry Regarding Gleason Score and Histomorphology Data in TCGA Prostate Adenocarcinoma (PanCancer Atlas)

Hi Melek, Thanks for contacting us. One way to identity such data is to 1. open all prostate cancer

Jun 30

Sadaf Abedi, JJ Gao2

Jun 30

absolute counts Vs alteration frequency

Hi Sadaf, Thanks for contacting us. The z-scores and related concepts are explained here: https://

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absolute counts Vs alteration frequency

Hi Sadaf, Thanks for contacting us. The z-scores and related concepts are explained here: https://

Jun 30

Francisco Penonori, JJ Gao2

Jun 30

Clarification Regarding TCGA Dataset Fields

Hi Francisco, Thanks for reporting this to us. I have logged the issue here: https://github.com/

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Clarification Regarding TCGA Dataset Fields

Hi Francisco, Thanks for reporting this to us. I have logged the issue here: https://github.com/

Jun 30

Melike Eray, JJ Gao2

Jun 30

Hi Melike, This link seems working for me. It might be a one-time glitch. Would you please try it

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Hi Melike, This link seems working for me. It might be a one-time glitch. Would you please try it

Jun 30

Charles Olowookere, JJ Gao2

Jun 30

cBioPortal API endpoint malfunctioning

Hi Charles, Thanks for contacting us. Please use entrezGeneIds instead of geneIds. You can try it out

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cBioPortal API endpoint malfunctioning

Hi Charles, Thanks for contacting us. Please use entrezGeneIds instead of geneIds. You can try it out

Jun 30

sabire kılıçarslan, Nikolaus Schultz3

Jun 26

Thank you 24 Haz 2025 Sal 22:40 tarihinde Nikolaus Schultz <nsch...@gmail.com> şunu yazdı:

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Thank you 24 Haz 2025 Sal 22:40 tarihinde Nikolaus Schultz <nsch...@gmail.com> şunu yazdı:

Jun 26

aryar...@gmail.com

Jun 26

Public study not showing up

Greetings, We recently moved our self hosted cBioportal instant from Docker to AKS at our institution

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Public study not showing up

Greetings, We recently moved our self hosted cBioportal instant from Docker to AKS at our institution

Jun 26

olofin daniel, Nikolaus Schultz2

Jun 24

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

Jun 24

Michele Kulesko, Nikolaus Schultz2

Jun 24

Visualization of Exon-Level CNAs in OncoPrint

Dear Michele, This is a great question. We do not currently have a way to encode these exon level

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Visualization of Exon-Level CNAs in OncoPrint

Dear Michele, This is a great question. We do not currently have a way to encode these exon level

Jun 24

Neurología CHUA, Nikolaus Schultz2

Jun 24

Help with survival analysis in cBioPortal for gene groups

Hi Gema, One way to do this is via the study view. In the example below I started with the study view

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Help with survival analysis in cBioPortal for gene groups

Hi Gema, One way to do this is via the study view. In the example below I started with the study view

Jun 24

Matteo Valerio, Aaron L2

Jun 23

Request to mention "pyBioPortal" on cBioPortal’s Web API Clients page

Hi Matteo, Thanks for reaching and and for developing this tool! We'll bring this up at our next

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Request to mention "pyBioPortal" on cBioPortal’s Web API Clients page

Hi Matteo, Thanks for reaching and and for developing this tool! We'll bring this up at our next

Jun 23

LUCILE MARIE PAULE JEUSSET, Nikolaus Schultz2

Jun 19

CNV discrepancy PanCancerAtlas vs GDC

Dear Lucile, Thank you for reaching out. I am not surprised that you see differences in copy-number

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CNV discrepancy PanCancerAtlas vs GDC

Dear Lucile, Thank you for reaching out. I am not surprised that you see differences in copy-number

Jun 19

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

Jun 18

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

Jun 18

Hao-Kuen Lin, Benjamin Gross3

Jun 16

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

Jun 16

HIROMI YANASE, Prasanna Jagannathan5

Jun 16

[cbioportal] Uploading public data

Hello Jag, Thank you for your support. I'll try to upload the data to my private cBioPortal.

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[cbioportal] Uploading public data

Hello Jag, Thank you for your support. I'll try to upload the data to my private cBioPortal.

Jun 16

Ji Hen Lau, Benjamin Gross3

Jun 15

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

Jun 15

Vincent Duchaos, Prasanna Jagannathan4

Jun 13

[On-prems instance] Unknown sample id found

Hi Vincent The usual convention is that each study will have its patients named as <studyname>-

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[On-prems instance] Unknown sample id found

Hi Vincent The usual convention is that each study will have its patients named as <studyname>-

Jun 13

母一丹, Prasanna Jagannathan2

Jun 12

Hi, Thanks for contacting the cbioportal google group. Is this error happening consistently? I was

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Hi, Thanks for contacting the cbioportal google group. Is this error happening consistently? I was

Jun 12

Fatemeh Shirazi, Prasanna Jagannathan2

Jun 11

Converting cBioPortal TARGET datasets to ANNOVAR format - VCF annotation showing no matches

Hi Fatemeh Thanks for contacting cBioPortal google group. In the Annovar commandline that was shared,

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Converting cBioPortal TARGET datasets to ANNOVAR format - VCF annotation showing no matches

Hi Fatemeh Thanks for contacting cBioPortal google group. In the Annovar commandline that was shared,

Jun 11

Ji Hen Lau, Prasanna Jagannathan5

Jun 11

MAF File Validation Warning - Variant_Classification Mapping Issues

Thanks for the clarification ! On Wed, 11 Jun 2025 at 23:46, Prasanna Jagannathan <jagnathan@gmail

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MAF File Validation Warning - Variant_Classification Mapping Issues

Thanks for the clarification ! On Wed, 11 Jun 2025 at 23:46, Prasanna Jagannathan <jagnathan@gmail

Jun 11

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