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cBioPortal for Cancer Genomics Discussion Group

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Seth Sadis, Ritika Kundra2

Nov 5

hg38 content in curated set of non-redundant studies

Thank you for reporting this. We have fixed the issue. Ritika On Wed, Nov 5, 2025 at 10:04 AM Seth

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hg38 content in curated set of non-redundant studies

Thank you for reporting this. We have fixed the issue. Ritika On Wed, Nov 5, 2025 at 10:04 AM Seth

Nov 5

Nicholas Henderson, Nikolaus Schultz2

Nov 5

Question about START_DATE in MSK Chord

Hi Nicholas, In the MSK-CHORD data set, all times are relative to when the tumor sample was sequenced

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Question about START_DATE in MSK Chord

Hi Nicholas, In the MSK-CHORD data set, all times are relative to when the tumor sample was sequenced

Nov 5

Rory Johnson, Zeynep Karagöz3

Nov 4

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.

Nov 4

╄→冷莫感, Tim Kuijpers2

Oct 30

there is a Error reporting

Dear, I am unable to reproduce the error when I click on the URL you shared. Could you confirm that

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there is a Error reporting

Dear, I am unable to reproduce the error when I click on the URL you shared. Could you confirm that

Oct 30

Oct 30

Working at cBioPortal

Hi cBioPortal team, I find the work that you are doing to be quite meaningful and would like to be a

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Working at cBioPortal

Hi cBioPortal team, I find the work that you are doing to be quite meaningful and would like to be a

Oct 30

Rebecca Sansale, Aaron L2

Oct 29

Clickhouse error

Hi Rebecca, Thanks for trying this out. Can you look at the web server log? it should have detail

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Clickhouse error

Hi Rebecca, Thanks for trying this out. Can you look at the web server log? it should have detail

Oct 29

frans frans, JJ Gao2

Oct 29

Downloading OncoKB Annotations from Mutations Page

Hi Frans, Thanks for reaching out. Sorry we will only be able to provide oncogenicity and levels

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Downloading OncoKB Annotations from Mutations Page

Hi Frans, Thanks for reaching out. Sorry we will only be able to provide oncogenicity and levels

Oct 29

李永心, Tali Mazor2

Oct 29

Hi - The link you shared is working for me. Could you try again and let us know if you continue to

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Hi - The link you shared is working for me. Could you try again and let us know if you continue to

Oct 29

elias, Baby Anusha Satravada2

Oct 28

Question regarding pdac_msk_2024 upload

Hi Elias, Thanks for sharing the validation log. The errors you're seeing in the data_sv.txt file

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Question regarding pdac_msk_2024 upload

Hi Elias, Thanks for sharing the validation log. The errors you're seeing in the data_sv.txt file

Oct 28

Yuqiong Song, … Tali Mazor4

Oct 28

Hi - The link you shared is working for me. Could you try again and let us know if you continue to

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Hi - The link you shared is working for me. Could you try again and let us know if you continue to

Oct 28

Arian Michael Daschner, Ritika Kundra3

Oct 23

Request for Information regarding the HPV Status in the TCGA-HNSC Dataset

Dear Ritika, thank you very much for your quick reply. In the cBioPortal study "Head and Neck

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Request for Information regarding the HPV Status in the TCGA-HNSC Dataset

Dear Ritika, thank you very much for your quick reply. In the cBioPortal study "Head and Neck

Oct 23

Sachin Kumar, JJ Gao2

Oct 22

Python API client to download mRNASeq data across all studies

You can download the data from our datahub in bulk. Please note that we have limited bandwidth for

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Python API client to download mRNASeq data across all studies

You can download the data from our datahub in bulk. Please note that we have limited bandwidth for

Oct 22

Sachin Kumar, JJ Gao4

Oct 22

mRNASeq Samples Collection

Hi Sachin, One way to get the number is to select the "Curated set of non-redundant studies

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mRNASeq Samples Collection

Hi Sachin, One way to get the number is to select the "Curated set of non-redundant studies

Oct 22

Oct 22

Tissue Sample Image files for local cbio instance (?)

Hi John, Yes, it is as straightforward as that. Please feel free to reach out to us if you have

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Tissue Sample Image files for local cbio instance (?)

Hi John, Yes, it is as straightforward as that. Please feel free to reach out to us if you have

Oct 22

Samuel Hawkins, JJ Gao2

Oct 22

Missing Genes in Datasets

Hi Sam, PREX1 is not part of the MSK-IMPACT gene panel - one way to check this is to look at the

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Missing Genes in Datasets

Hi Sam, PREX1 is not part of the MSK-IMPACT gene panel - one way to check this is to look at the

Oct 22

Jane Liang, Nikolaus Schultz2

Oct 22

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

Oct 22

Brendan Veeneman, JJ Gao2

Oct 22

Hi Brendan, Thank you very much for bringing this to our attention. We had an issue in the last data

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Hi Brendan, Thank you very much for bringing this to our attention. We had an issue in the last data

Oct 22

Raja Anand, JJ Gao2

Oct 20

A sincere request for your assistance in resolving an issue.

Hi Raajesh, It was due to a data issue we are working on. Sorry for the inconvenience. We'll get

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A sincere request for your assistance in resolving an issue.

Hi Raajesh, It was due to a data issue we are working on. Sorry for the inconvenience. We'll get

Oct 20

Y Chen, JJ Gao2

Oct 20

how to integrate Cancer Digital Slide Archive (CDSA) into local cbioportal?

Dear Yingfei, The cBioPortal CDSI integration is simply an i-frame to the CDSA website (https://

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how to integrate Cancer Digital Slide Archive (CDSA) into local cbioportal?

Dear Yingfei, The cBioPortal CDSI integration is simply an i-frame to the CDSA website (https://

Oct 20

T Nishanth, JJ Gao2

Oct 17

Study Sample Question

Dear T Nishanth, Thanks for reaching out to us. You can save your cohorts as groups. See tutorials [1

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Study Sample Question

Dear T Nishanth, Thanks for reaching out to us. You can save your cohorts as groups. See tutorials [1

Oct 17

Florian Andersch, … SKANDERUP Anders Martin Jacobsen7

Oct 17

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

ARES PRIVATE Thanks, Yes, this issue has been flagged previously – caused by the copy number caller

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

ARES PRIVATE Thanks, Yes, this issue has been flagged previously – caused by the copy number caller

Oct 17

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

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