cBioPortal for Cancer Genomics Discussion Group

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Deya Alzoubi, Priti Kumari2

12/6/22

loading my data

Hi Deya, Unfortunately, we do not have such an example. Depending on your data source you could write

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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 Kumari2

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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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 Kumari3

12/12/22

Assistance with an analysis

Hi Jeniffer, You can use cBioPortal's Group Comparison feature for such queries. For more

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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 Kumari2

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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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 Kumari2

12/6/22

sv/fusion mutations

Hi, SV = structural variants/fusion are mutations resulting from chromosomal rearrangements, large

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sv/fusion mutations

Hi, SV = structural variants/fusion are mutations resulting from chromosomal rearrangements, large

12/6/22

Chan, Aimee, Priti Kumari2

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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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 Kumari4

12/8/22

Thank you a lot. These answers were very helpful! Am Mittwoch, 7. Dezember 2022 um 20:35:00 MEZ hat

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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 Gross2

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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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.org3

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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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.org2

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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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 Schultz4

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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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 Sheridan3

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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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.org2

11/18/22

Hi Takafumi NAKANE, Thanks for reaching out! We have this in most of the mutation data files: ・Number

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Hi Takafumi NAKANE, Thanks for reaching out! We have this in most of the mutation data files: ・Number

11/18/22

Peter Saffrey, … Peter Saffrey4

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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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 L3

11/14/22

MutationMapper Issue

Hi Alessandro, There seems to be an issue with reference genome in your data. We use Ensemble's

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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.org2

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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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.org2

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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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.org2

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:

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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 Schultz2

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

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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.org4

11/18/22

Hi Shivani, Thanks for reaching out! Not entirely sure what schema you are looking for, but here are

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Hi Shivani, Thanks for reaching out! Not entirely sure what schema you are looking for, but here are

11/18/22

Johannes Veihelmann, Nikolaus Schultz2

11/10/22

Msk 2022 sarcoma study

Hi Johannes, There is no expression information available for that data set - only targeted DNA

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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.org2

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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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 Singh2

11/14/22

Detailed Information

Hi Shivani, The information you are looking for can be found by visiting the associated publication.

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Detailed Information

Hi Shivani, The information you are looking for can be found by visiting the associated publication.

11/14/22

Tulasi S, Jessica Singh4

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

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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 L2

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

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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 Hagen2

11/10/22

Hi Rana, The network tab has been replaced a couple of years ago I believe. I hope the pathway tab

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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 Saffrey3

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

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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 Singh5

11/14/22

More Information

Hi Shivani, cBioPortal has 363 studies available (182904 samples). You can find cBioPortal's

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More Information

Hi Shivani, cBioPortal has 363 studies available (182904 samples). You can find cBioPortal's

11/14/22

Tulasi S, … Cyriac Kandoth16

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

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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 Gross3

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

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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

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