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cBioPortal for Cancer Genomics Discussion Group
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cBioPortal for Cancer Genomics Discussion Group
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Deya Alzoubi
,
Priti Kumari
2
12/6/22
loading my data
Hi Deya, Unfortunately, we do not have such an example. Depending on your data source you could write
unread,
Completed
loading my data
Hi Deya, Unfortunately, we do not have such an example. Depending on your data source you could write
12/6/22
eric...@tongji.edu.cn
,
Priti Kumari
2
12/7/22
Sample Size Variance Consulting
Hi Lin Ye, It's possible that not all samples had a mutation event. The cohort includes 1661
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Completed
Sample Size Variance Consulting
Hi Lin Ye, It's possible that not all samples had a mutation event. The cohort includes 1661
12/7/22
Alexander, Jennifer
,
Priti Kumari
3
12/12/22
Assistance with an analysis
Hi Jeniffer, You can use cBioPortal's Group Comparison feature for such queries. For more
unread,
Completed
Assistance with an analysis
Hi Jeniffer, You can use cBioPortal's Group Comparison feature for such queries. For more
12/12/22
alaa sleman
,
Priti Kumari
2
12/8/22
group comparison data
Hi Alaa, If you have the list of patient IDs, you can go to the study view, click on "Custom
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Completed
group comparison data
Hi Alaa, If you have the list of patient IDs, you can go to the study view, click on "Custom
12/8/22
zgonzalez
,
Priti Kumari
2
12/6/22
sv/fusion mutations
Hi, SV = structural variants/fusion are mutations resulting from chromosomal rearrangements, large
unread,
Completed
sv/fusion mutations
Hi, SV = structural variants/fusion are mutations resulting from chromosomal rearrangements, large
12/6/22
Chan, Aimee
,
Priti Kumari
2
12/2/22
Hosting data for academic use
Hi Aimee, Thank you for reaching out. Please refer to our documentation here for guidance on how to
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Completed
Hosting data for academic use
Hi Aimee, Thank you for reaching out. Please refer to our documentation here for guidance on how to
12/2/22
Chiara L.
,
Priti Kumari
4
12/8/22
Own Data
Thank you a lot. These answers were very helpful! Am Mittwoch, 7. Dezember 2022 um 20:35:00 MEZ hat
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Completed
Own Data
Thank you a lot. These answers were very helpful! Am Mittwoch, 7. Dezember 2022 um 20:35:00 MEZ hat
12/8/22
Thierry Soussi
,
Benjamin Gross
2
11/21/22
MSK patient sample ID
Hi Thierry, T01 means this is the first tumor sample sequenced belonging to the patient. IM6 is the
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Completed
MSK patient sample ID
Hi Thierry, T01 means this is the first tumor sample sequenced belonging to the patient. IM6 is the
11/21/22
Kadie Hudson
,
debr...@mskcc.org
3
11/18/22
Re: Co-Expression Analysis and RNA count data
Great! Glad you found it! Thanks! Ino From: 'Kadie Hudson' via cBioPortal for Cancer Genomics
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Completed
Re: Co-Expression Analysis and RNA count data
Great! Glad you found it! Thanks! Ino From: 'Kadie Hudson' via cBioPortal for Cancer Genomics
11/18/22
Aqsa Arshad
,
debr...@mskcc.org
2
11/18/22
cBioPortal Query
Hi Aqsa Arshad, Thanks for reaching out! Not all studies in cBioPortal have MSS information. We do
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Completed
cBioPortal Query
Hi Aqsa Arshad, Thanks for reaching out! Not all studies in cBioPortal have MSS information. We do
11/18/22
Francesco Tamiro
, …
Nikolaus Schultz
4
11/18/22
Cannot replicate RNA expression comparison between studies
Hi Francesco, We still have this functionality for the TCGA Pan Cancer Atlas studies. Try the link
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Completed
Cannot replicate RNA expression comparison between studies
Hi Francesco, We still have this functionality for the TCGA Pan Cancer Atlas studies. Try the link
11/18/22
Joseph, Greg
,
Robert Sheridan
3
11/17/22
cBioPortal - ICD10 Codes
Sorry .. 2 quick corrections: This: "The file format for data_clinical_sample.txt describe the
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Completed
cBioPortal - ICD10 Codes
Sorry .. 2 quick corrections: This: "The file format for data_clinical_sample.txt describe the
11/17/22
Takafumi NAKANE
,
debr...@mskcc.org
2
11/18/22
About CNA
Hi Takafumi NAKANE, Thanks for reaching out! We have this in most of the mutation data files: ・Number
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Completed
About CNA
Hi Takafumi NAKANE, Thanks for reaching out! We have this in most of the mutation data files: ・Number
11/18/22
Peter Saffrey
, …
Peter Saffrey
4
11/21/22
Uploading GENIE; problems with MySQL lock table
Hi Ino, I'm happy to have a go at adding Redis to the docker-compose configuration, which does
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Completed
Uploading GENIE; problems with MySQL lock table
Hi Ino, I'm happy to have a go at adding Redis to the docker-compose configuration, which does
11/21/22
ALESSANDRO LIQUORI
,
Aaron L
3
11/14/22
MutationMapper Issue
Hi Alessandro, There seems to be an issue with reference genome in your data. We use Ensemble's
unread,
Completed
MutationMapper Issue
Hi Alessandro, There seems to be an issue with reference genome in your data. We use Ensemble's
11/14/22
ASHAAR NABIL AL-AKHRAS
,
debr...@mskcc.org
2
11/18/22
Synapse GENIE Data Access Request
Hi Ashaar N. Al-Akhras, Thanks for reaching out! You can download all the GENIE data from Synapse:
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Completed
Synapse GENIE Data Access Request
Hi Ashaar N. Al-Akhras, Thanks for reaching out! You can download all the GENIE data from Synapse:
11/18/22
lu...@mskcc.org
,
debr...@mskcc.org
2
11/18/22
Question about cbioportal data access
Hi Josie, Apologies about the delay in getting back to you – do you still see this? Forwarding to
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Completed
Question about cbioportal data access
Hi Josie, Apologies about the delay in getting back to you – do you still see this? Forwarding to
11/18/22
Irina Leonardi
,
debr...@mskcc.org
2
11/18/22
Error with survival analysis
Hi Irina, Thanks for reaching out! Is it still crashing for you? The query is working for me now:
unread,
Completed
Error with survival analysis
Hi Irina, Thanks for reaching out! Is it still crashing for you? The query is working for me now:
11/18/22
Seungtea Kim
,
Nikolaus Schultz
2
11/14/22
Mutation in Deep deletion
Hi, This is a good question, and multiple factors could play a role here: 1) Copy-number calling is
unread,
Completed
Mutation in Deep deletion
Hi, This is a good question, and multiple factors could play a role here: 1) Copy-number calling is
11/14/22
shivani gupta
, …
debr...@mskcc.org
4
11/18/22
No of Datasets
Hi Shivani, Thanks for reaching out! Not entirely sure what schema you are looking for, but here are
unread,
Completed
No of Datasets
Hi Shivani, Thanks for reaching out! Not entirely sure what schema you are looking for, but here are
11/18/22
Johannes Veihelmann
,
Nikolaus Schultz
2
11/10/22
Msk 2022 sarcoma study
Hi Johannes, There is no expression information available for that data set - only targeted DNA
unread,
Completed
Msk 2022 sarcoma study
Hi Johannes, There is no expression information available for that data set - only targeted DNA
11/10/22
John Francis
,
debr...@mskcc.org
2
11/18/22
metaImport.py --- error during load --- Expected to find 1 script *.jar , but found 0
Hi John Apologies for the delay - did you find a solution for this? Thanks! Ino From: cbioportal@
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Completed
metaImport.py --- error during load --- Expected to find 1 script *.jar , but found 0
Hi John Apologies for the delay - did you find a solution for this? Thanks! Ino From: cbioportal@
11/18/22
Shivani Gupta
,
Jessica Singh
2
11/14/22
Detailed Information
Hi Shivani, The information you are looking for can be found by visiting the associated publication.
unread,
Completed
Detailed Information
Hi Shivani, The information you are looking for can be found by visiting the associated publication.
11/14/22
Tulasi S
,
Jessica Singh
4
11/22/22
Example dataset where tSNE, UMAP and PCA have been visualized
Thank you Jessica for your reply. Will look into the example and get back to you if I have any
unread,
Completed
Example dataset where tSNE, UMAP and PCA have been visualized
Thank you Jessica for your reply. Will look into the example and get back to you if I have any
11/22/22
Afshin Raouf
,
Aaron L
2
11/9/22
Error retrieving data
THanks for this report Afrshin. Can you try the same page to see if the problem persists? Looks to me
unread,
Completed
Error retrieving data
THanks for this report Afrshin. Can you try the same page to see if the problem persists? Looks to me
11/9/22
Rana Salah
,
Sjoerd van Hagen
2
11/10/22
network tab
Hi Rana, The network tab has been replaced a couple of years ago I believe. I hope the pathway tab
unread,
Completed
network tab
Hi Rana, The network tab has been replaced a couple of years ago I believe. I hope the pathway tab
11/10/22
Peter Saffrey
, …
Peter Saffrey
3
11/16/22
PORTAL_HOME in docker deployment
Hi Luke, Thanks for your reply. I actually found this in the meantime by looking more closely at the
unread,
Completed
PORTAL_HOME in docker deployment
Hi Luke, Thanks for your reply. I actually found this in the meantime by looking more closely at the
11/16/22
shivani gupta
, …
Jessica Singh
5
11/14/22
More Information
Hi Shivani, cBioPortal has 363 studies available (182904 samples). You can find cBioPortal's
unread,
Completed
More Information
Hi Shivani, cBioPortal has 363 studies available (182904 samples). You can find cBioPortal's
11/14/22
Tulasi S
, …
Cyriac Kandoth
16
11/19/22
Allele frequency not seen
Thanks a lot for your clarification @Cyriac Kandoth.. On Sun, Nov 20, 2022, 1:51 AM Cyriac Kandoth
unread,
Completed
Allele frequency not seen
Thanks a lot for your clarification @Cyriac Kandoth.. On Sun, Nov 20, 2022, 1:51 AM Cyriac Kandoth
11/19/22
Xiaoli Zhang
,
Benjamin Gross
3
8/30/22
Installation help with docker-compose
Hello again, It was some internal system setting issues. It is fixed now. Thanks for your suggestions
unread,
Completed
Installation help with docker-compose
Hello again, It was some internal system setting issues. It is fixed now. Thanks for your suggestions
8/30/22