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cBioPortal for Cancer Genomics Discussion Group
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Ian Atol
,
Benjamin Gross
2
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
unread,
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.org
5
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
unread,
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 Gross
2
Jan 26
mrna data access on swaggerClient
Hi Kristen, You can construct an http request within python which complies with one of the following
unread,
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 Gross
3
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
unread,
[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 Gross
2
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.org
2
Jan 25
GSOC 2023
Hi Parteek, Thanks for reaching out! We will apply again for GSoC but Google will announce only Feb
unread,
GSOC 2023
Hi Parteek, Thanks for reaching out! We will apply again for GSoC but Google will announce only Feb
Jan 25
Joseph, Greg
, …
Benjamin Gross
4
Jan 24
Local cBioPortal instance - data question
Hi Ekaterina, Unfortunately, we have not had a chance to provide this behavior. Best, -Benjamin On
unread,
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.org
2
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.
unread,
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 Mazor
2
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.com
2
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 Gross
2
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
unread,
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 Gross
13
Jan 23
Keycloak
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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Keycloak
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 Gross
2
Jan 23
Tutorial Resources
Hi, You can find links to a our collection of tutorials/webinars here: https://docs.cbioportal.org/
unread,
Tutorial Resources
Hi, You can find links to a our collection of tutorials/webinars here: https://docs.cbioportal.org/
Jan 23
Balaji Krishnamachary
,
Tali Mazor
3
Jan 19
Hi Balaji, It looks like we're using a student's t-test for the mRNA expression comparison on
unread,
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 Mazor
2
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 Mazor
6
Jan 18
Question
That is totally understandable. Thank you for your quick and prompt reply. You and your team didn
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Question
That is totally understandable. Thank you for your quick and prompt reply. You and your team didn
Jan 18
Bayan Abu Al-Ragheb
,
Tali Mazor
2
Jan 18
TCGA Datasets
Hi Bayan, In short, the different TCGA datasets generally include the same samples, but differ in
unread,
TCGA Datasets
Hi Bayan, In short, the different TCGA datasets generally include the same samples, but differ in
Jan 18
Yue Zhang
,
Tali Mazor
3
Jan 18
Downloading SNV Data
Hi Yue, My original answer was for data available on cbioportal.org. For GENIE data, you can download
unread,
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 Mazor
2
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 Mazor
2
Jan 17
PM1 criteria - somatic mutation hotspot
Hi Joyce, I'm not sure I understand your question. We cannot provide guidance on the ACMG
unread,
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 Mazor
2
Jan 17
Custom plots for microbiome signatures
Hi Lennart, Integrating a custom visualization into cBioPortal requires editing the frontend code for
unread,
Custom plots for microbiome signatures
Hi Lennart, Integrating a custom visualization into cBioPortal requires editing the frontend code for
Jan 17
Dorian Forte
,
Tali Mazor
2
Jan 17
Information about custom analysis
Hi Dorian, We do not provide a support service like this for cBioPortal. Instead, I encourage you to
unread,
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 L
2
Jan 17
error
Thanks for this report Daniela, Did the error occur on load of the page or after some interaction? On
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error
Thanks for this report Daniela, Did the error occur on load of the page or after some interaction? On
Jan 17
Giorgia Gandolfi
, …
Aaron Atkinson
4
Jan 13
empty CNA gene panel
Could you elaborate? Are the GISTIC results there? When you open the “all_thresholded.by_genes.txt”
unread,
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.org
2
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:
unread,
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.org
2
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
unread,
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 L
9
Jan 10
User Authentication
Hi John, Ok, I consulted with some coworkers. We do not support any kind of "basic auth".
unread,
User Authentication
Hi John, Ok, I consulted with some coworkers. We do not support any kind of "basic auth".
Jan 10
M B
,
Matthijs Pon
2
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
unread,
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 Hagen
4
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
unread,
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