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de Bruijn, Ino
, …
Harry Sun
10
5:45 PM
Re: [cbioportal] Can cbioportal continue to support non-docker version?
Hi Jeremy Cbioportal-core does not work. I run into no class found. If you look at its
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Re: [cbioportal] Can cbioportal continue to support non-docker version?
Hi Jeremy Cbioportal-core does not work. I run into no class found. If you look at its
5:45 PM
Qi Wang
,
JJ Gao
3
5:11 PM
Query gene mutations in tripe negative breast cancer
Many thanks! From: JJ Gao <jianji...@gmail.com> Date: Monday, May 6, 2024 at 4:18 PM To: Qi
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Query gene mutations in tripe negative breast cancer
Many thanks! From: JJ Gao <jianji...@gmail.com> Date: Monday, May 6, 2024 at 4:18 PM To: Qi
5:11 PM
Rini Pauly
,
de Bruijn, Ino
3
4:30 PM
Annotating illumina Dragen Fusion calls
Thank you, I think we would need help with the breakpoints and Exon numbers too. I am attaching a
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Annotating illumina Dragen Fusion calls
Thank you, I think we would need help with the breakpoints and Exon numbers too. I am attaching a
4:30 PM
Deepak Roshan VG
9:43 AM
How to BMI details for Breast cancer studies from TCGA or Cbio portal
Hi From where I can details of BMI for braest cancer patients from TCGA or Cbio portal data set
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How to BMI details for Breast cancer studies from TCGA or Cbio portal
Hi From where I can details of BMI for braest cancer patients from TCGA or Cbio portal data set
9:43 AM
Abhishek Reddy
,
Gaofei Zhao
2
May 3
500 error - explore selected studies
Hi Abhishek, I tried following the documentation here. I can see the study lgg_ucsf_2014 shows up
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500 error - explore selected studies
Hi Abhishek, I tried following the documentation here. I can see the study lgg_ucsf_2014 shows up
May 3
Shiya Song
,
JJ Gao
4
May 3
Does Cbioportal support olink/somalogic data
Hi Shiya, You would need to code the times in the timeline format [1]. Please see example below [2] -
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Does Cbioportal support olink/somalogic data
Hi Shiya, You would need to code the times in the timeline format [1]. Please see example below [2] -
May 3
Justin Levens
,
Priti Kumari
3
May 3
Datahub public data not visible after import
Hell Priti, Thanks for the suggestion, but I think the issue is something else. Upon further
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Datahub public data not visible after import
Hell Priti, Thanks for the suggestion, but I think the issue is something else. Upon further
May 3
Anurag Saxena
,
Saxena, Anurag
3
May 3
How to add Institute logo to the right
It worked. Thank you so much. FWIW the location in v5.4.10 is $PORTAL_HOME/portal/src/main/resources/
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How to add Institute logo to the right
It worked. Thank you so much. FWIW the location in v5.4.10 is $PORTAL_HOME/portal/src/main/resources/
May 3
Cnu
,
de Bruijn, Ino
4
May 2
Orien Cbioportal data access using API
Thank you, will send an email to see if they can share any information. On Thursday, May 2, 2024 at
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Orien Cbioportal data access using API
Thank you, will send an email to see if they can share any information. On Thursday, May 2, 2024 at
May 2
Alpatov, Roman
May 2
question about the miRNA clusters, mRNA clusters, and exon imbalance score
Hello, I am working on comparing the subsets of data with variable AR gene expression and in the tab
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question about the miRNA clusters, mRNA clusters, and exon imbalance score
Hello, I am working on comparing the subsets of data with variable AR gene expression and in the tab
May 2
Qi, Yuwei
, …
Ramya Madupuri
7
May 1
TCGA PanCancer Altas Radiation treatment details
Hi Ramya, Got it! Thank you for clarifying. Best, Yuwei From: Ramya Madupuri <ramyamadupuri99@
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TCGA PanCancer Altas Radiation treatment details
Hi Ramya, Got it! Thank you for clarifying. Best, Yuwei From: Ramya Madupuri <ramyamadupuri99@
May 1
Srivatsan V
, …
JJ Gao
5
May 1
Error when using seedDB with hg38 support
Hi Lucia, Thanks for the suggestion. Yes, we will make it the default. -JJ On Wed, May 1, 2024 at 4:
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Error when using seedDB with hg38 support
Hi Lucia, Thanks for the suggestion. Yes, we will make it the default. -JJ On Wed, May 1, 2024 at 4:
May 1
Bosc L
,
Nikolaus Schultz
2
Apr 30
Somatic vs. germline cBioportal mutation
Hi, None of the MSK-IMPACT studies ion cbioportal.org contain germline variants. Only somatic
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Somatic vs. germline cBioportal mutation
Hi, None of the MSK-IMPACT studies ion cbioportal.org contain germline variants. Only somatic
Apr 30
Nicki Frontera
,
Priti Kumari
2
Apr 29
Examining More Than 1 Driver Mutation in a Dataset
Hi Nicki, You can use OQL to query for driver mutations for 26 genes of interest. Once you have the
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Examining More Than 1 Driver Mutation in a Dataset
Hi Nicki, You can use OQL to query for driver mutations for 26 genes of interest. Once you have the
Apr 29
Kate Ignatius
,
Priti Kumari
2
Apr 29
IDs
Hi Kate, You cannot match the MBC Project samples with TCGA. They are different datasets. Please,
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IDs
Hi Kate, You cannot match the MBC Project samples with TCGA. They are different datasets. Please,
Apr 29
Miller, Michael L.
,
Nikolaus Schultz
3
Apr 29
TERT promoter dataset - PMID 33285287
Thanks. From: Nikolaus Schultz <nsch...@gmail.com> Sent: Thursday, April 25, 2024 8:38 PM To:
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TERT promoter dataset - PMID 33285287
Thanks. From: Nikolaus Schultz <nsch...@gmail.com> Sent: Thursday, April 25, 2024 8:38 PM To:
Apr 29
Badal Roy
,
Priti Kumari
2
Apr 26
Uploading-Analyzing public/personal data
Hi Badal, You can install your own cBioPortal instance to analyze your NGS data: https://docs.
unread,
Uploading-Analyzing public/personal data
Hi Badal, You can install your own cBioPortal instance to analyze your NGS data: https://docs.
Apr 26
Samuel Kellen
, …
Tim Kuijpers
5
Apr 26
Unable to iniitalize cBioPortal off Docker
Hello, Tim I've tried redoing the steps from the documentation after purging the images and
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Unable to iniitalize cBioPortal off Docker
Hello, Tim I've tried redoing the steps from the documentation after purging the images and
Apr 26
SHI, YUFEI
,
Schultz, Nikolaus
2
Apr 26
RE: Reminder# cBioportal# OS for (Col6a3) by using cBioportal & KM plotter
Hi, Do both tools use the same threshold to define over-expression? That may explain the differences.
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RE: Reminder# cBioportal# OS for (Col6a3) by using cBioportal & KM plotter
Hi, Do both tools use the same threshold to define over-expression? That may explain the differences.
Apr 26
Kwiatkowski, David J.,MD, PhD
,
Nikolaus Schultz
7
Apr 26
Structural variants on Genie cbio
Just a clarification. Below is what the table looks like after filtering for Peritoneal Mesothelioma
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Structural variants on Genie cbio
Just a clarification. Below is what the table looks like after filtering for Peritoneal Mesothelioma
Apr 26
Badal Sharma 211908
Apr 25
i need a queary of 26 gene for my pan cancer analysis
HDAC6, TLE1, TLE4, SFRP1, APC, TCF7L1, WIF1, TLE2, DKK1, TCF7L2, AXIN1, SFRP2, LRP5, TCF7, TLE3,
unread,
i need a queary of 26 gene for my pan cancer analysis
HDAC6, TLE1, TLE4, SFRP1, APC, TCF7L1, WIF1, TLE2, DKK1, TCF7L2, AXIN1, SFRP2, LRP5, TCF7, TLE3,
Apr 25
Choe, Michelle
,
Benjamin Gross
3
Apr 25
Open Pediatric Cancer Project
Hello, Thank you so much for responding! I realized I was just on the wrong site and the study I
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Open Pediatric Cancer Project
Hello, Thank you so much for responding! I realized I was just on the wrong site and the study I
Apr 25
Rafi Danino
,
Benjamin Gross
2
Apr 25
expanding my dataset
Hi Rafi, Thank you for your patience. You can use the data type search box to narrow down studies by
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expanding my dataset
Hi Rafi, Thank you for your patience. You can use the data type search box to narrow down studies by
Apr 25
nhodge
Apr 25
Lung Squamous cell Carcinoma
Good Morning, Does the data type copy number come from dna sequencing or are they inferred in
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Lung Squamous cell Carcinoma
Good Morning, Does the data type copy number come from dna sequencing or are they inferred in
Apr 25
Tebon, Peyton
,
Nikolaus Schultz
3
Apr 24
Sarcoma panel sequencing for cBioPortal
Hi Niki, Thanks for the quick response! We will review the data formats you linked and get our data
unread,
Sarcoma panel sequencing for cBioPortal
Hi Niki, Thanks for the quick response! We will review the data formats you linked and get our data
Apr 24
Ikhapoh, Izuagie
,
Nikolaus Schultz
3
Apr 24
Bladder cancer datasets
Hi Niki, Thank you. This helps. Best, Izuagie. Get Outlook for iOS From: Nikolaus Schultz <
unread,
Bladder cancer datasets
Hi Niki, Thank you. This helps. Best, Izuagie. Get Outlook for iOS From: Nikolaus Schultz <
Apr 24
Daiana Toader - QIAGEN
,
Avery Wang
2
Apr 24
https://www.cbioportal.org/webservice.do?cmd=getCancerStudies not working
Good morning Daiana, `Webservice.do` was deprecated with the latest release of cBioPortal. If you
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https://www.cbioportal.org/webservice.do?cmd=getCancerStudies not working
Good morning Daiana, `Webservice.do` was deprecated with the latest release of cBioPortal. If you
Apr 24
김주원
,
Nikolaus Schultz
3
Apr 24
Issues with Displaying Mutations in Mutation Mapper
Thank you! It has been completely resolved. It's all thanks to you :) 2024년 4월 24일 수요일 오후 9시 17분
unread,
Issues with Displaying Mutations in Mutation Mapper
Thank you! It has been completely resolved. It's all thanks to you :) 2024년 4월 24일 수요일 오후 9시 17분
Apr 24
Bill
Apr 24
SAML setting up_Cbioportal version and Keycloak version
Hi, I have two questions: 1) I set up SAML using cBioportal 5.4.10 and keycloak:4.8.3.Final. Is this
unread,
SAML setting up_Cbioportal version and Keycloak version
Hi, I have two questions: 1) I set up SAML using cBioportal 5.4.10 and keycloak:4.8.3.Final. Is this
Apr 24
Shayna Simonstein
,
Avery Wang
3
Apr 23
Downloading data from sarcoma_msk_2022 (7494 patients)
Great, thank you so much for checking Avery! On Monday, April 22, 2024 at 9:32:00 AM UTC-4 Avery Wang
unread,
Downloading data from sarcoma_msk_2022 (7494 patients)
Great, thank you so much for checking Avery! On Monday, April 22, 2024 at 9:32:00 AM UTC-4 Avery Wang
Apr 23