cBioPortal for Cancer Genomics Discussion Group

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Zenovia Gonzalez, Nikolaus Schultz2

Nov 29

PLD1 mutations - reading the types of mutations

Hi Zenovia, We categorize all nonsense and frameshift mutations as truncating. Splice mutations are

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PLD1 mutations - reading the types of mutations

Hi Zenovia, We categorize all nonsense and frameshift mutations as truncating. Splice mutations are

Nov 29

김두호 / 학생 / 국제농업기술학과, … Ritika Kundra4

Nov 29

Question about data mismatches

Hi Dooho, Our fusion data comes from a curated paper (https://pubmed.ncbi.nlm.nih.gov/29617662/)

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Question about data mismatches

Hi Dooho, Our fusion data comes from a curated paper (https://pubmed.ncbi.nlm.nih.gov/29617662/)

Nov 29

Peter Saffrey, mram...@gmail.com3

Nov 29

Hi Marcel, Thanks for the response. My Python code looks like this: profileId = f"{study_name}

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Hi Marcel, Thanks for the response. My Python code looks like this: profileId = f"{study_name}

Nov 29

Ahmad Saqib, Aaron L3

Nov 28

Some functions are not working in oncoprintjs library

Hi Aaron, When I am using onconprint.setZoom(x,y) function and passing the number values of x and y,

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Some functions are not working in oncoprintjs library

Hi Aaron, When I am using onconprint.setZoom(x,y) function and passing the number values of x and y,

Nov 28

Rahul Sanawar, Tali Mazor4

Nov 23

Query regarding the units of expression on Y-axis.

Hi Tali, I could not get the answer from the reply. I tried to click on the link you shared for mRNA

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Query regarding the units of expression on Y-axis.

Hi Tali, I could not get the answer from the reply. I tried to click on the link you shared for mRNA

Nov 23

Daniela Rotin, Tali Mazor3

Nov 23

analyzing cancer alteration in splice variants

Hi Daniela, I see - as you noted, cBioPortal does not support querying based on a specific isoform.

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analyzing cancer alteration in splice variants

Hi Daniela, I see - as you noted, cBioPortal does not support querying based on a specific isoform.

Nov 23

Tulasi S, Jessica Singh4

Nov 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

Nov 22

Thierry Soussi, Benjamin Gross2

Nov 21

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

Nov 21

Nov 21

patient ID code for patient from MSK-impact

I can't find anymore the code used for patients from mSK exemple P-0044860-T01-IM6 I known that P

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patient ID code for patient from MSK-impact

I can't find anymore the code used for patients from mSK exemple P-0044860-T01-IM6 I known that P

Nov 21

Peter Saffrey, … Peter Saffrey4

Nov 21

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

Nov 21

Carlos Espinosa, Aaron L2

Nov 19

Timeline Question

Hi Carlos, The appearance of those attributes on the clinical data tab is an oversight on our part.

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Timeline Question

Hi Carlos, The appearance of those attributes on the clinical data tab is an oversight on our part.

Nov 19

Tulasi S, … Cyriac Kandoth16

Nov 19

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

Nov 19

Gill,Jonathan Benjamin, … Suzuki,Erika3

Nov 19

Clinical data on pediatric cancer studies

Great thank you, appreciate the help. Thank you, Erika On Nov 18, 2022, at 5:51 PM, debruiji@mskcc.

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Clinical data on pediatric cancer studies

Great thank you, appreciate the help. Thank you, Erika On Nov 18, 2022, at 5:51 PM, debruiji@mskcc.

Nov 19

Francesco Tamiro, … Nikolaus Schultz4

Nov 18

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

Nov 18

Kadie Hudson, debr...@mskcc.org3

Nov 18

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

Nov 18

John Francis, debr...@mskcc.org2

Nov 18

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@

Nov 18

Irina Leonardi, debr...@mskcc.org2

Nov 18

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:

Nov 18

shivani gupta, … debr...@mskcc.org4

Nov 18

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

Nov 18

lu...@mskcc.org, debr...@mskcc.org2

Nov 18

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

Nov 18

ASHAAR NABIL AL-AKHRAS, debr...@mskcc.org2

Nov 18

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:

Nov 18

Takafumi NAKANE, debr...@mskcc.org2

Nov 18

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

Nov 18

Aqsa Arshad, debr...@mskcc.org2

Nov 18

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

Nov 18

Joseph, Greg, Robert Sheridan3

Nov 17

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

Nov 17

Nov 16

portal.properties -- how do you tell which one is being used by the web app?

I did a search on for the portal.properties file on our server and found that it exists in multiple

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portal.properties -- how do you tell which one is being used by the web app?

I did a search on for the portal.properties file on our server and found that it exists in multiple

Nov 16

Peter Saffrey, … Peter Saffrey3

Nov 16

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

Nov 16

MARCHAIS ANTONIN, … kun...@mskcc.org5

Nov 16

About MAPPYACTS showcase dataset in cbioportal.org

Dear Ritika, Sorry for my late reply, none of these times are compatible with my agenda. When are you

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About MAPPYACTS showcase dataset in cbioportal.org

Dear Ritika, Sorry for my late reply, none of these times are compatible with my agenda. When are you

Nov 16

ALESSANDRO LIQUORI, Aaron L3

Nov 14

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

Nov 14

Seungtea Kim, Nikolaus Schultz2

Nov 14

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

Nov 14

Shivani Gupta, Jessica Singh2

Nov 14

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.

Nov 14

shivani gupta, … Jessica Singh5

Nov 14

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

Nov 14

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