cBioPortal for Cancer Genomics Discussion Group

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Julia Baaske, Benjamin Gross3

Aug 19

Discrepancy between Study numbers and Cancer Type numbers

Hi Julia, I think what may be going on with the query in question (https://bit.ly/3Ayk2tT ) is that

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Discrepancy between Study numbers and Cancer Type numbers

Hi Julia, I think what may be going on with the query in question (https://bit.ly/3Ayk2tT ) is that

Aug 19

Xiaoli Zhang, Benjamin Gross2

Aug 19

Installation help with docker-compose

Hi Xiaoli, Its clear from the log snippet that the cbioportal-session-database (used by the

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Installation help with docker-compose

Hi Xiaoli, Its clear from the log snippet that the cbioportal-session-database (used by the

Aug 19

James Costello, … debr...@mskcc.org3

Aug 19

API documentation link down

Thanks for reporting! Fixed the link in the documentation: https://www.cbioportal.org/api/swagger-ui/

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API documentation link down

Thanks for reporting! Fixed the link in the documentation: https://www.cbioportal.org/api/swagger-ui/

Aug 19

Aug 18

Help! data_mrna_seq_v2_rsem_zscores_ref_all_samples

Hi, I'm having issues finding a clear answer or description of how this data was normalized:

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Help! data_mrna_seq_v2_rsem_zscores_ref_all_samples

Hi, I'm having issues finding a clear answer or description of how this data was normalized:

Aug 18

Aug 18

[cbioportal] about mRNA Expression z-Scores (RNA Seq V2 RSEM)

Hi Luisa, Yes, we log transformed the data before calculating zscore in

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[cbioportal] about mRNA Expression z-Scores (RNA Seq V2 RSEM)

Hi Luisa, Yes, we log transformed the data before calculating zscore in

Aug 18

Peixin Dong, Benjamin Gross2

Aug 18

Regarding Select Genomic Profiles

Hi Peixin, mRNA expression z-scores relative to all samples are computed expression z-scores (log-

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Regarding Select Genomic Profiles

Hi Peixin, mRNA expression z-scores relative to all samples are computed expression z-scores (log-

Aug 18

이호선, Hongxin Zhang2

Aug 18

There was an error retrieving data.

Hi Hosun, Sorry about the issue. We had some instability issues with OncoKB which should be fixed now

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There was an error retrieving data.

Hi Hosun, Sorry about the issue. We had some instability issues with OncoKB which should be fixed now

Aug 18

Fabián Robledo, Luke Sikina3

Aug 16

Doubts in survival plots covariates

Hi Luke, Thank you so much for your answer. That was exactly what I was looking for. Fabián Robledo

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Doubts in survival plots covariates

Hi Luke, Thank you so much for your answer. That was exactly what I was looking for. Fabián Robledo

Aug 16

Aaron Atkinson, Sjoerd van Hagen2

Aug 10

generic_assay_type: TREATMENT_RESPONSE

Hi Aaron, If you are referring to the treatment response datatype described here, then by default it

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generic_assay_type: TREATMENT_RESPONSE

Hi Aaron, If you are referring to the treatment response datatype described here, then by default it

Aug 10

gemma antonucci, Tali Mazor3

Aug 10

assistance oncoprint

Hi Gemma, It looks like your data is not in the appropriate format. It looks like you are providing

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assistance oncoprint

Hi Gemma, It looks like your data is not in the appropriate format. It looks like you are providing

Aug 10

Samriddhi Gupta, Luke Sikina2

Aug 10

Trouble in accessing data via Bravado

Hi Samriddhi, I'm unfamiliar with Bravado - if you reply to this thread with more information

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Trouble in accessing data via Bravado

Hi Samriddhi, I'm unfamiliar with Bravado - if you reply to this thread with more information

Aug 10

Michael Weist, debr...@mskcc.org2

Aug 7

Dear Dr Weist, Thanks for reaching out! We currently only support downloading of expression data of

unread,

Dear Dr Weist, Thanks for reaching out! We currently only support downloading of expression data of

Aug 7

TAKADA YUKA / 高田有佳, debr...@mskcc.org3

Aug 7

Question about a error in a on-premises cBioPortal

Hi Yuka Takada, Glad you were able to resolve it! Let us know if you have any other questions Best

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Question about a error in a on-premises cBioPortal

Hi Yuka Takada, Glad you were able to resolve it! Let us know if you have any other questions Best

Aug 7

whit...@mskcc.org, debr...@mskcc.org3

Aug 4

IMPACT 505 gene panel coding

Hi Karissa, Thanks for reaching out! That's odd indeed I'm CC'ing the curation team on

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IMPACT 505 gene panel coding

Hi Karissa, Thanks for reaching out! That's odd indeed I'm CC'ing the curation team on

Aug 4

Metitiri, Ediri E, debr...@mskcc.org2

Aug 4

cBioPortal: Out of date mapping?

Hi Ediri, Thanks for reaching out! Although the cBioPortal software supports hg38 the currently

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cBioPortal: Out of date mapping?

Hi Ediri, Thanks for reaching out! Although the cBioPortal software supports hg38 the currently

Aug 4

MSK INTERN, … Sjoerd van Hagen4

Aug 3

Comparing gene signatures

Hi Alan, Depending on what you would like to do, here are some options: - You probably know that you

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Comparing gene signatures

Hi Alan, Depending on what you would like to do, here are some options: - You probably know that you

Aug 3

Rita Glazer, debr...@mskcc.org2

Aug 2

Using cBioPortal to Visualize Data

Hi Rita, Thanks for reaching out! I am not super familiar with REV1 and Tumor Lysis Syndrome (TLS) in

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Using cBioPortal to Visualize Data

Hi Rita, Thanks for reaching out! I am not super familiar with REV1 and Tumor Lysis Syndrome (TLS) in

Aug 2

Silke Appenzeller, Sander Rodenburg4

Aug 2

cBioportal datasets

Hi Silke, We are currently experiencing issues in the public studies on Datahub and the validator.

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cBioportal datasets

Hi Silke, We are currently experiencing issues in the public studies on Datahub and the validator.

Aug 2

Katsap Smazhenyi

Aug 2

missing miRNA genes prevent imports

Hi, I am trying to import the datahub data into cBioPortal deployed via docker. Some of the imports

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missing miRNA genes prevent imports

Hi, I am trying to import the datahub data into cBioPortal deployed via docker. Some of the imports

Aug 2

Oliver Langenhorn, Elena Garcia Lara6

Aug 2

import from datahub fails

Hi, It seems there is no WXS panel in the link your provided, and that's the panel that is

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import from datahub fails

Hi, It seems there is no WXS panel in the link your provided, and that's the panel that is

Aug 2

Aditi Gulati, Aaron L5

Jul 29

Oops. There was an error retrieving data

Hi Aaron, Thanks for your prompt help! Session-service had stopped running. We had this issue with

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Oops. There was an error retrieving data

Hi Aaron, Thanks for your prompt help! Session-service had stopped running. We had this issue with

Jul 29

Lindsey Mortensen, … Nikolaus Schultz3

Jul 26

Normal tissue mRNA seq source

Hi Lindsey, Just to add: The normal samples used by the different TCGA projects are healthy tissue

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Normal tissue mRNA seq source

Hi Lindsey, Just to add: The normal samples used by the different TCGA projects are healthy tissue

Jul 26

Vaishali Chakraborty, … kun...@mskcc.org14

Jul 25

Doubt regarding CN analysis

Hi Ritika, Thank you for your help. Have a great week! Best regards, Vaishali On Fri, 22 Jul 2022 at

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Doubt regarding CN analysis

Hi Ritika, Thank you for your help. Have a great week! Best regards, Vaishali On Fri, 22 Jul 2022 at

Jul 25

niels bohr, JJ Gao2

Jul 22

Whole Gene Deletions

Hi Niels, I am wondering if you can import the whole gene deletions as copy number events? Best, -JJ

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Whole Gene Deletions

Hi Niels, I am wondering if you can import the whole gene deletions as copy number events? Best, -JJ

Jul 22

Owen Prall, JJ Gao2

Jul 22

cbioportal/GENIE data to aid histopathology diagnosis

Hi Owen, Thanks for contacting us. For looking at combinations of genes and variants, one option is

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cbioportal/GENIE data to aid histopathology diagnosis

Hi Owen, Thanks for contacting us. For looking at combinations of genes and variants, one option is

Jul 22

Alexandra Nicole Demetriou, JJ Gao4

Jul 21

Issue searching gene expression

Hi Alexandra, You would need the arm-level CNA data in order to do that analysis. For example, in

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Issue searching gene expression

Hi Alexandra, You would need the arm-level CNA data in order to do that analysis. For example, in

Jul 21

Dave DeStephano, David Higgins4

Jul 21

Download all mutations

Hello , We are continuing to investigate options for defining genes of interest. Do you have any

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Download all mutations

Hello , We are continuing to investigate options for defining genes of interest. Do you have any

Jul 21

Jeremy Cumbo, … Sjoerd van Hagen3

Jul 21

How to capture metadata about cBioPortal instance usage?

Hi Jeremy, We use Matomo for tracking users. This is an open source application that you can deploy

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How to capture metadata about cBioPortal instance usage?

Hi Jeremy, We use Matomo for tracking users. This is an open source application that you can deploy

Jul 21

谷口源太郎, JJ Gao2

Jul 20

Question about Firehose data

Hi Gentaro, The Firehose data and the TCGA published data (inluding the PanCancer Atlas ones) are

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Question about Firehose data

Hi Gentaro, The Firehose data and the TCGA published data (inluding the PanCancer Atlas ones) are

Jul 20

Ian Lackie, debr...@mskcc.org2

Jul 19

SQL error on new cBioportal install - "Table 'cbioportal.genetic_profile' doesn't exist"

Hi Ian, Thanks for reaching out! Apologies for the delay. Sorry you are having issues with the

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SQL error on new cBioportal install - "Table 'cbioportal.genetic_profile' doesn't exist"

Hi Ian, Thanks for reaching out! Apologies for the delay. Sorry you are having issues with the

Jul 19

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