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Nikolas Balanis
,
Tali Mazor
2
5:30 PM
Cannot recreate dashboard mutation data with data from datasets tab
Hi Niko, Thanks for reaching out and for the very detailed explanation of what you've done! I
unread,
Cannot recreate dashboard mutation data with data from datasets tab
Hi Niko, Thanks for reaching out and for the very detailed explanation of what you've done! I
5:30 PM
内田士朗
,
Tali Mazor
2
3:58 PM
Inquiry about Neoplasm Histologic Grade in the METABRIC Dataset on cBioPortal
Hi Shiro, Thanks for reaching out. The clinical data in cBioPortal, including histologic grade, comes
unread,
Inquiry about Neoplasm Histologic Grade in the METABRIC Dataset on cBioPortal
Hi Shiro, Thanks for reaching out. The clinical data in cBioPortal, including histologic grade, comes
3:58 PM
idanoy
,
Tali Mazor
2
3:52 PM
creation of dataset
Hi Idan, We do have an API you can query in python, and there is python client developed by another
unread,
creation of dataset
Hi Idan, We do have an API you can query in python, and there is python client developed by another
3:52 PM
Janae Matthews
,
Nikolaus Schultz
2
Mar 16
Inquiry
Hi, Amplifications (and deletions) are defined at the DNA copy-number level, completely independent
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Inquiry
Hi, Amplifications (and deletions) are defined at the DNA copy-number level, completely independent
Mar 16
TASI ZH
,
Nikolaus Schultz
2
Mar 16
cBioPortal user reported error
Hi, The link provided seems to work for me, without an error message. Can you please check to see if
unread,
cBioPortal user reported error
Hi, The link provided seems to work for me, without an error message. Can you please check to see if
Mar 16
Waryszak Marcin
, …
Benjamin Gross
15
Mar 15
SAML Problem
I had to rebuild and start all session service dependencies (mongod + session-service) and all api/
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SAML Problem
I had to rebuild and start all session service dependencies (mongod + session-service) and all api/
Mar 15
Mr Xiao Zhang
Mar 14
Query Comparison/Survival of Multiple Individual Genes
Hi, I was wondering if there is a way to query comparison/survival data for manyindividual genes
unread,
Query Comparison/Survival of Multiple Individual Genes
Hi, I was wondering if there is a way to query comparison/survival data for manyindividual genes
Mar 14
Fangyang
, …
James Robinson
4
Mar 14
Setting up igv view of segments without connection to uscs.edu or other network
Thanks James and JJ, I see the reference genome tracks is defined in the "genomes.json"
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Setting up igv view of segments without connection to uscs.edu or other network
Thanks James and JJ, I see the reference genome tracks is defined in the "genomes.json"
Mar 14
smahase
,
Nikolaus Schultz
2
Mar 7
Inquiry Regarding Amplification of PLD1 Gene in Lung Squamous Cell Carcinoma
Hi, “Amplification” refers to additional copies of DNA. You can assess the expression of your genes
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Inquiry Regarding Amplification of PLD1 Gene in Lung Squamous Cell Carcinoma
Hi, “Amplification” refers to additional copies of DNA. You can assess the expression of your genes
Mar 7
Bekir Ergüner
, …
Fangyang
5
Mar 6
Disable Mane transcript tracks
Hi, I'm trying to modify the igv behavior and come across this post. Where can I find the config
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Disable Mane transcript tracks
Hi, I'm trying to modify the igv behavior and come across this post. Where can I find the config
Mar 6
Mann, Aleesa
,
Nikolaus Schultz
5
Mar 5
Data Dictionary
Thank you, Niki, for sharing this link. I will review it and follow up with any questions I may have.
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Data Dictionary
Thank you, Niki, for sharing this link. I will review it and follow up with any questions I may have.
Mar 5
Maija Kohonen-Corish
,
Priti Kumari
2
Mar 4
Microbiome data in cBioPortal
Hi Miaja, You can visualize microbiome data by clicking on Charts here: https://www.cbioportal.org/
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Microbiome data in cBioPortal
Hi Miaja, You can visualize microbiome data by clicking on Charts here: https://www.cbioportal.org/
Mar 4
Baikunth Dwivedy
,
Nikolaus Schultz
2
Mar 4
Citing cBioportal
Hi, You can find guidelines on how to acknowledged the use of TCGA data here. In this case, you can
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Citing cBioportal
Hi, You can find guidelines on how to acknowledged the use of TCGA data here. In this case, you can
Mar 4
Bekir Ergüner
,
Benjamin Gross
6
Mar 1
Structural variants API endpoint
Bekir, I think its safe to use the endpoint found in the internal definition. Internal is meant for
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Structural variants API endpoint
Bekir, I think its safe to use the endpoint found in the internal definition. Internal is meant for
Mar 1
Andrew Blake
,
kalletl...@gmail.com
2
Mar 1
How do I turn off the Pathways tab on a patient view
Hi Andrew, Currently Pathways tab on a patient view is show all the time. the above configurations
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How do I turn off the Pathways tab on a patient view
Hi Andrew, Currently Pathways tab on a patient view is show all the time. the above configurations
Mar 1
Alyssa Richman
,
Tali Mazor
6
Feb 29
HM27 axis units?
Hi again, Here is an update on what I have figured out. Based on the TARGET documentation it seems
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HM27 axis units?
Hi again, Here is an update on what I have figured out. Based on the TARGET documentation it seems
Feb 29
David
,
Priti Kumari
3
Feb 29
Regarding Clinvar Data
Genome Nexus public API. On Thursday 29 February 2024 at 23:41:18 UTC+5:30 Priti Kumari wrote: Hi
unread,
Regarding Clinvar Data
Genome Nexus public API. On Thursday 29 February 2024 at 23:41:18 UTC+5:30 Priti Kumari wrote: Hi
Feb 29
Veera Ojala
, …
Aaron L
11
Feb 28
samples missing when making a query with 4 genes instead of 1 of those 4
Thank you. One more thing that I've been trying to figure out but haven't yet: Is it possible
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samples missing when making a query with 4 genes instead of 1 of those 4
Thank you. One more thing that I've been trying to figure out but haven't yet: Is it possible
Feb 28
Emanuele Loro
,
Benjamin Gross
3
Feb 27
Information request
Thanks Benjamin, This is very useful. I have been asked to check about the possibility of having a
unread,
Information request
Thanks Benjamin, This is very useful. I have been asked to check about the possibility of having a
Feb 27
Rong “Rosetta” Jiang
,
Benjamin Gross
2
Feb 27
log2FC is 0 for significant genes
Hi Rong, Can you provide me with the URL to your query? Thanks, Benjamin On Feb 26, 2024, at 12:10 PM
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log2FC is 0 for significant genes
Hi Rong, Can you provide me with the URL to your query? Thanks, Benjamin On Feb 26, 2024, at 12:10 PM
Feb 27
flo...@pwdrgate.com
,
Nikolaus Schultz
3
Feb 27
An introduction to Mulberry Biolabs and PowderGate Discovery - a philantropic venture fund dedicated to pediatric glioma
Hi Nikolaus – I'm eager to follow up on the addition of pediatric glioma data to cBioportal and
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An introduction to Mulberry Biolabs and PowderGate Discovery - a philantropic venture fund dedicated to pediatric glioma
Hi Nikolaus – I'm eager to follow up on the addition of pediatric glioma data to cBioportal and
Feb 27
Stefan Werner
,
Benjamin Gross
2
Feb 23
cBioPortal user reported error
Hi Stefan, Can you provide what query you were making that resulted in this error? Best, -Benjamin On
unread,
cBioPortal user reported error
Hi Stefan, Can you provide what query you were making that resulted in this error? Best, -Benjamin On
Feb 23
de Bruijn, Ino
, …
Harry Sun
9
Feb 22
Re: [cbioportal] Can cbioportal continue to support non-docker version?
Jeremy, Thank you for your update. I will look at its difference. Harry On Thu, Feb 22, 2024 at 7:43
unread,
Re: [cbioportal] Can cbioportal continue to support non-docker version?
Jeremy, Thank you for your update. I will look at its difference. Harry On Thu, Feb 22, 2024 at 7:43
Feb 22
Hamid Ghaedi
,
Matthijs Pon
5
Feb 21
Docker deployment issue: Datbase connection ?
Thanks Matthijs for your input. I have figured out to run the portal and below I am posting the
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Docker deployment issue: Datbase connection ?
Thanks Matthijs for your input. I have figured out to run the portal and below I am posting the
Feb 21
Manuel Ramos
,
jagn...@gmail.com
2
Feb 21
Downloading data from MSK-IMPACT dataset
Hi Manuel, The dataset information for the entire study can be downloaded from the below link. https:
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Downloading data from MSK-IMPACT dataset
Hi Manuel, The dataset information for the entire study can be downloaded from the below link. https:
Feb 21
Hernandez_Tiedra.Sonia
,
jagn...@gmail.com
2
Feb 21
How to generate groups in CBioportal using a list of samples with Depmap ID
Hi Sonia Thanks for your question. It is possible to create groups using DepMap Id. Create a list of
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How to generate groups in CBioportal using a list of samples with Depmap ID
Hi Sonia Thanks for your question. It is possible to create groups using DepMap Id. Create a list of
Feb 21
Almog Kedem
, …
Anjali Sheahan
4
Feb 20
cbioportalR problems
Hi, I am having the same issue. On Tuesday, February 20, 2024 at 12:17:53 PM UTC-5 de Bruijn, Ino
unread,
cbioportalR problems
Hi, I am having the same issue. On Tuesday, February 20, 2024 at 12:17:53 PM UTC-5 de Bruijn, Ino
Feb 20
Alpatov, Roman
, …
de Bruijn, Ino
11
Feb 16
question about comparison of gene expression of a subset of genes in a specific tumor or across several tumors.
HI Ino, Thanks for the follow up. The question I wanted to address would be to look at the difference
unread,
question about comparison of gene expression of a subset of genes in a specific tumor or across several tumors.
HI Ino, Thanks for the follow up. The question I wanted to address would be to look at the difference
Feb 16
Waryszak Marcin
, …
Jeremy Easton-Marks
6
Feb 16
Non dockerised instance
That's great to hear. I just added some documentation that will allow you to run the newest
unread,
Non dockerised instance
That's great to hear. I just added some documentation that will allow you to run the newest
Feb 16
Y Chen
, …
Kevin Doyle
6
Feb 15
keycloak docker container doesn't work
Hi Kevin, I'm in the step of setting up the https ssl certificates. Our cbioportal is using
unread,
keycloak docker container doesn't work
Hi Kevin, I'm in the step of setting up the https ssl certificates. Our cbioportal is using
Feb 15