cBioPortal for Cancer Genomics Discussion Group

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Ian Atol, Benjamin Gross2

Jan 26

SAML Infinite Redirects

Hi Ian, Can you provide a log file from the webservice? It should be able to provide an indication of

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SAML Infinite Redirects

Hi Ian, Can you provide a log file from the webservice? It should be able to provide an indication of

Jan 26

Hadyn Tang, … Satr...@mskcc.org5

Jan 26

SV Second Gene Incorrect OncoPrint & Broken Mutation/Download tabs

Dear Baby Anusha, Thanks for your help! Unfortunately I got an error about the JVM running out of

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SV Second Gene Incorrect OncoPrint & Broken Mutation/Download tabs

Dear Baby Anusha, Thanks for your help! Unfortunately I got an error about the JVM running out of

Jan 26

Kristen Nader, Benjamin Gross2

Jan 26

mrna data access on swaggerClient

Hi Kristen, You can construct an http request within python which complies with one of the following

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mrna data access on swaggerClient

Hi Kristen, You can construct an http request within python which complies with one of the following

Jan 26

She, Ruicong, Benjamin Gross3

Jan 26

[cBioPortal] hg38 CNA data is not showing

Hi Benjamin, Thank you so much for the quick reply. I did as you instructed but the CNA box is still

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[cBioPortal] hg38 CNA data is not showing

Hi Benjamin, Thank you so much for the quick reply. I did as you instructed but the CNA box is still

Jan 26

Joseph, Greg, Benjamin Gross2

Jan 25

"Hugo symbols not known to cBioPortal" error that shouldn't be

Hi Greg, I'm guessing you are using the metaImport.py script to import your data (https://docs.

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"Hugo symbols not known to cBioPortal" error that shouldn't be

Hi Greg, I'm guessing you are using the metaImport.py script to import your data (https://docs.

Jan 25

Parteek Goyal, debr...@mskcc.org2

Jan 25

Hi Parteek, Thanks for reaching out! We will apply again for GSoC but Google will announce only Feb

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Hi Parteek, Thanks for reaching out! We will apply again for GSoC but Google will announce only Feb

Jan 25

Joseph, Greg, … Benjamin Gross4

Jan 24

Local cBioPortal instance - data question

Hi Ekaterina, Unfortunately, we have not had a chance to provide this behavior. Best, -Benjamin On

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Local cBioPortal instance - data question

Hi Ekaterina, Unfortunately, we have not had a chance to provide this behavior. Best, -Benjamin On

Jan 24

Aditi Gulati, debr...@mskcc.org2

Jan 24

Issue with clickable link on cBioPortal local instance home page

Hi Aditi, Thanks for reaching out! We use this functionality for one of our portals: https://genie.

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Issue with clickable link on cBioPortal local instance home page

Hi Aditi, Thanks for reaching out! We use this functionality for one of our portals: https://genie.

Jan 24

Rowyn Liebau, Tali Mazor2

Jan 24

Survival comparison High vs low expression

Hi Rowyn, There are two ways you can approach this. If you run a query, which sounds like the

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Survival comparison High vs low expression

Hi Rowyn, There are two ways you can approach this. If you run a query, which sounds like the

Jan 24

Parl, Fritz, ramyama...@gmail.com2

Jan 24

possible discrepancy

Hi Fritz, Are you querying for these samples in the PanCancer Atlas datasets? Can you share the link

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possible discrepancy

Hi Fritz, Are you querying for these samples in the PanCancer Atlas datasets? Can you share the link

Jan 24

Amin Nematbakhsh

Jan 23

Ontologies/vocabularies used for your clinical attributes

Dear Madam or Sir, I am writing to you to inquire about the ontologies/vocabularies for the clinical

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Ontologies/vocabularies used for your clinical attributes

Dear Madam or Sir, I am writing to you to inquire about the ontologies/vocabularies for the clinical

Jan 23

naomi....@jfcr.or.jp, Benjamin Gross2

Jan 23

cBioPortal user reported error

Hi, This link is loading for me. Are you still having this issue? I'm wondering if it would be

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cBioPortal user reported error

Hi, This link is loading for me. Are you still having this issue? I'm wondering if it would be

Jan 23

John Francis, … Benjamin Gross13

Jan 23

Thank you On Monday, January 23, 2023 at 4:07:02 PM UTC-5 Benjamin Gross wrote: Oh, but I see an IP

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Thank you On Monday, January 23, 2023 at 4:07:02 PM UTC-5 Benjamin Gross wrote: Oh, but I see an IP

Jan 23

Olatunji, Olalekan, Benjamin Gross2

Jan 23

Tutorial Resources

Hi, You can find links to a our collection of tutorials/webinars here: https://docs.cbioportal.org/

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Tutorial Resources

Hi, You can find links to a our collection of tutorials/webinars here: https://docs.cbioportal.org/

Jan 23

Balaji Krishnamachary, Tali Mazor3

Jan 19

Hi Balaji, It looks like we're using a student's t-test for the mRNA expression comparison on

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Hi Balaji, It looks like we're using a student's t-test for the mRNA expression comparison on

Jan 19

Francesco Antonio Tucci, Tali Mazor2

Jan 19

missing mRNAseq zscores_ref_normal_samples in TCGA-PAAD

Hi Francesco, Thanks for letting us know. I've created an issue in GitHub to add this option -

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missing mRNAseq zscores_ref_normal_samples in TCGA-PAAD

Hi Francesco, Thanks for letting us know. I've created an issue in GitHub to add this option -

Jan 19

Khushman, Moh'd, Tali Mazor6

Jan 18

That is totally understandable. Thank you for your quick and prompt reply. You and your team didn

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That is totally understandable. Thank you for your quick and prompt reply. You and your team didn

Jan 18

Bayan Abu Al-Ragheb, Tali Mazor2

Jan 18

Hi Bayan, In short, the different TCGA datasets generally include the same samples, but differ in

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Hi Bayan, In short, the different TCGA datasets generally include the same samples, but differ in

Jan 18

Yue Zhang, Tali Mazor3

Jan 18

Downloading SNV Data

Hi Yue, My original answer was for data available on cbioportal.org. For GENIE data, you can download

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Downloading SNV Data

Hi Yue, My original answer was for data available on cbioportal.org. For GENIE data, you can download

Jan 18

Vokes,Natalie, Tali Mazor2

Jan 17

New dataset from MDACC

Hi Natalie, Thanks for reaching out. I've cc'ed our head curator, Ritika, who can better

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New dataset from MDACC

Hi Natalie, Thanks for reaching out. I've cc'ed our head curator, Ritika, who can better

Jan 17

Joyce El Hokayem, Tali Mazor2

Jan 17

PM1 criteria - somatic mutation hotspot

Hi Joyce, I'm not sure I understand your question. We cannot provide guidance on the ACMG

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PM1 criteria - somatic mutation hotspot

Hi Joyce, I'm not sure I understand your question. We cannot provide guidance on the ACMG

Jan 17

Lennart Graf, Tali Mazor2

Jan 17

Custom plots for microbiome signatures

Hi Lennart, Integrating a custom visualization into cBioPortal requires editing the frontend code for

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Custom plots for microbiome signatures

Hi Lennart, Integrating a custom visualization into cBioPortal requires editing the frontend code for

Jan 17

Dorian Forte, Tali Mazor2

Jan 17

Information about custom analysis

Hi Dorian, We do not provide a support service like this for cBioPortal. Instead, I encourage you to

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Information about custom analysis

Hi Dorian, We do not provide a support service like this for cBioPortal. Instead, I encourage you to

Jan 17

DANIELA NICOLE ROJAS ESPINOZA, Aaron L2

Jan 17

Thanks for this report Daniela, Did the error occur on load of the page or after some interaction? On

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Thanks for this report Daniela, Did the error occur on load of the page or after some interaction? On

Jan 17

Giorgia Gandolfi, … Aaron Atkinson4

Jan 13

empty CNA gene panel

Could you elaborate? Are the GISTIC results there? When you open the “all_thresholded.by_genes.txt”

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empty CNA gene panel

Could you elaborate? Are the GISTIC results there? When you open the “all_thresholded.by_genes.txt”

Jan 13

Santosh Dudhabhate, debr...@mskcc.org2

Jan 13

Need more information about gene expression (Prostate Adenocarcinoma (TCGA, Firehose Legacy)

Hi Santosh, Thanks for reaching out! For that specific TCGA study one can find more information here:

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Need more information about gene expression (Prostate Adenocarcinoma (TCGA, Firehose Legacy)

Hi Santosh, Thanks for reaching out! For that specific TCGA study one can find more information here:

Jan 13

Julia Sidorova, debr...@mskcc.org2

Jan 13

a question about non coding RNA sequencing data

Hi Julia, Thanks for reaching out! Just a caveat: I am not very familiar with satellite analysis but

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a question about non coding RNA sequencing data

Hi Julia, Thanks for reaching out! Just a caveat: I am not very familiar with satellite analysis but

Jan 13

John Francis, Aaron L9

Jan 10

User Authentication

Hi John, Ok, I consulted with some coworkers. We do not support any kind of "basic auth".

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User Authentication

Hi John, Ok, I consulted with some coworkers. We do not support any kind of "basic auth".

Jan 10

M B, Matthijs Pon2

Jan 10

mRNA Expression: z-score to diploid or all samples

Hi, This is the link to the explanations for the Z-Score calculations. I've summarised below them

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mRNA Expression: z-score to diploid or all samples

Hi, This is the link to the explanations for the Z-Score calculations. I've summarised below them

Jan 10

Celina São José, Sjoerd van Hagen4

Jan 9

Survival analysis using copy-number data

Hi Celina, Glad that was helpful! I am not sure what you mean by selecting samples for specific

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Survival analysis using copy-number data

Hi Celina, Glad that was helpful! I am not sure what you mean by selecting samples for specific

Jan 9

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