cBioPortal for Cancer Genomics Discussion Group

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Brewer, Takae, Nikolaus Schultz2

Jan 19

cBioportal RNA-seq analysis

Hi, This manuscript probably has the best description of the batch correction applied to the TCGA

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cBioportal RNA-seq analysis

Hi, This manuscript probably has the best description of the batch correction applied to the TCGA

Jan 19

Uhrig, Sebastian, Benjamin Gross10

Jan 19

Import of fusions/structural variants

Hi Sebastian, Just wanted to keep you in the loop regarding our SV data refactoring. We've been

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Import of fusions/structural variants

Hi Sebastian, Just wanted to keep you in the loop regarding our SV data refactoring. We've been

Jan 19

bront...@gmail.com, Ino de Bruijn3

Jan 19

https://repo.spring.io/... Unauthorized

Ino, All is working now. Many thanks. bront On Wednesday, January 12, 2022 at 6:58:11 PM UTC-5 Ino de

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https://repo.spring.io/... Unauthorized

Ino, All is working now. Many thanks. bront On Wednesday, January 12, 2022 at 6:58:11 PM UTC-5 Ino de

Jan 19

Abhay Kanodia, Nikolaus Schultz2

Jan 18

selecting samples with desired mutations

Hi Abhay, Unfortunately, there is no one step-way to get the overlapping cases. An easy way to get

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selecting samples with desired mutations

Hi Abhay, Unfortunately, there is no one step-way to get the overlapping cases. An easy way to get

Jan 18

Eugene Bolotin, ramyama...@gmail.com2

Jan 18

cBioportal RNA-seq values in RPKM question

Hi Eugene, Thanks for reaching out! For sclc_ucologne_2015 study, the transcript information for RPKM

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cBioportal RNA-seq values in RPKM question

Hi Eugene, Thanks for reaching out! For sclc_ucologne_2015 study, the transcript information for RPKM

Jan 18

Ishan Dusane, … Sjoerd van Hagen7

Jan 17

Feature Development

Hi Ishan, I would say that if you want to have that list for your own database, it will be easiest to

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Feature Development

Hi Ishan, I would say that if you want to have that list for your own database, it will be easiest to

Jan 17

Rotraud Wieser, JJ Gao6

Jan 17

Several questions

Got it - I have create another ticket for that: https://github.com/cBioPortal/cbioportal/issues/9228

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Several questions

Got it - I have create another ticket for that: https://github.com/cBioPortal/cbioportal/issues/9228

Jan 17

Jan 14

authorities table

Hi there, I have created authorities and groups. I have this value set- always_show_study_group=

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authorities table

Hi there, I have created authorities and groups. I have this value set- always_show_study_group=

Jan 14

Gui, Hongxing, debr...@mskcc.org3

Jan 13

select and create new group from selected samples

Hi Simon, Hope all is well! Let us know if you still see this issue – happy to help debug Thanks! Ino

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select and create new group from selected samples

Hi Simon, Hope all is well! Let us know if you still see this issue – happy to help debug Thanks! Ino

Jan 13

Marialena Pouliou, Aaron Lisman4

Jan 12

Glad to hear the problem resolved. Seems possible it had to do with different accounts. Let us know

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Glad to hear the problem resolved. Seems possible it had to do with different accounts. Let us know

Jan 12

Raymond Perigo, … Pim van Nierop4

Jan 12

RBAC with SAML/Keycloak

Hi Ray, The feature you request is not on the development road map. Perhaps the built-in fine grained

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RBAC with SAML/Keycloak

Hi Ray, The feature you request is not on the development road map. Perhaps the built-in fine grained

Jan 12

Sasha Dagayev, debr...@mskcc.org2

Jan 12

cBio Cancer API Python Wrapper

Hi Sasha! Thanks for reaching out! That looks like a great project! We have two slacks: one for

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cBio Cancer API Python Wrapper

Hi Sasha! Thanks for reaching out! That looks like a great project! We have two slacks: one for

Jan 12

Jintian Chen (Student), JJ Gao3

Jan 11

Can cBioPortal show statistical significance?

Thanks a lot! Get Outlook for iOS From: JJ Gao <jianjiong.gao@gmail.com> Sent: Wednesday,

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Can cBioPortal show statistical significance?

Thanks a lot! Get Outlook for iOS From: JJ Gao <jianjiong.gao@gmail.com> Sent: Wednesday,

Jan 11

Shing Ho Vincent Chan, JJ Gao2

Jan 11

Inquiry on downloading the data

Hi Vincent, There are various options to download data in the various pages. The most convenient way

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Inquiry on downloading the data

Hi Vincent, There are various options to download data in the various pages. The most convenient way

Jan 11

debr...@mskcc.org

Jan 10

Re: [cbioportal] TCGA dataset question

Dear Dr Benej, Thanks for reaching out! Apologies about the delay in getting back to you For the TCGA

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Re: [cbioportal] TCGA dataset question

Dear Dr Benej, Thanks for reaching out! Apologies about the delay in getting back to you For the TCGA

Jan 10

NICHOLAS R RYDZEWSKI

Jan 9

cBioPortal RNASeq questions

Hello, my name is Nick Rydzewski and I appreciate all the work you have put into the cBioPortal

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cBioPortal RNASeq questions

Hello, my name is Nick Rydzewski and I appreciate all the work you have put into the cBioPortal

Jan 9

Jan 5

Definitive instructions for https setup

Hi I have seen a few people asking for help in setting up cbioportal + Keycloak + reverse-proxy (

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Definitive instructions for https setup

Hi I have seen a few people asking for help in setting up cbioportal + Keycloak + reverse-proxy (

Jan 5

Weiss Glen, … kun...@mskcc.org4

Jan 4

Study in the queue?

Great thank you On Jan 3, 2022, at 11:17 AM, kundrar@mskcc.org wrote: Hi Glen, Yes this study is on

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Study in the queue?

Great thank you On Jan 3, 2022, at 11:17 AM, kundrar@mskcc.org wrote: Hi Glen, Yes this study is on

Jan 4

carlos.es...@gmail.com, … Pim van Nierop15

Jan 4

Extra MAF columns not displayed on the Mutations tab

Hello Clement, I am still waiting for the pull requests to be merged. All the best, Pim On Tue, Jan 4

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Extra MAF columns not displayed on the Mutations tab

Hello Clement, I am still waiting for the pull requests to be merged. All the best, Pim On Tue, Jan 4

Jan 4

Ba Nguyen, pr...@ds.dfci.harvard.edu3

Jan 3

Expression data for UCSD Armor dataset

Hello, I believe this is a private dataset only available at the UCSD cBioPortal instance and not on

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Expression data for UCSD Armor dataset

Hello, I believe this is a private dataset only available at the UCSD cBioPortal instance and not on

Jan 3

12/30/21

TCGA dataset question

Good afternoon, We are browsing through the TCGA curated PanCancer datasets and found one particular

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TCGA dataset question

Good afternoon, We are browsing through the TCGA curated PanCancer datasets and found one particular

12/30/21

谢剑竹, … Ritika Kundra4

12/28/21

What's the meaning of "Somatic Status" in the file of "data_clinical _sample.txt"?

Hi Xie, The somatic status refers to if a sample in the study has a matched normal or not. Let us

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What's the meaning of "Somatic Status" in the file of "data_clinical _sample.txt"?

Hi Xie, The somatic status refers to if a sample in the study has a matched normal or not. Let us

12/28/21

Vlachavas, Efstathios-Iason, Ritika Kundra2

12/28/21

Which column between Tumor_Seq_Allele1 vs. Tumor_Seq_Allele2 to select in TCGA MAF files from cBioPortal for the "alteration column allele" for re-annotation purposes?

Hi Efstathios, Apologies for the delay. For annotation, please consider Reference Allele and Tumor

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Which column between Tumor_Seq_Allele1 vs. Tumor_Seq_Allele2 to select in TCGA MAF files from cBioPortal for the "alteration column allele" for re-annotation purposes?

Hi Efstathios, Apologies for the delay. For annotation, please consider Reference Allele and Tumor

12/28/21

Younsoo Kang, … debr...@mskcc.org7

12/28/21

Regarding query by gene error

Great to hear! Let us know if there is anything else we can help with. If you have a few minutes, we

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Regarding query by gene error

Great to hear! Let us know if there is anything else we can help with. If you have a few minutes, we

12/28/21

Aditi Gulati, … Aaron Lisman6

12/23/21

log4j library security issue

Hi Pablo, Thanks for the alert . We just yesterday released a portal version with upgrade to 2.17.0.

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log4j library security issue

Hi Pablo, Thanks for the alert . We just yesterday released a portal version with upgrade to 2.17.0.

12/23/21

Konstantin Chernyshov, Sjoerd van Hagen3

12/23/21

cbioportal installation and customization

Hi Konstantin, It seems your question has gone unnoticed somehow, sorry about that. I think what you

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cbioportal installation and customization

Hi Konstantin, It seems your question has gone unnoticed somehow, sorry about that. I think what you

12/23/21

Christopher Ryan Douglas, sanderrodenburg2

12/22/21

(CPTAC, Cell 2021) - No Phosphoproteasome functionality

Hi Chris, This dropdown does actually work, but because of the number of entries behind this menu,

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(CPTAC, Cell 2021) - No Phosphoproteasome functionality

Hi Chris, This dropdown does actually work, but because of the number of entries behind this menu,

12/22/21

Matthew Simcock (Student), Sander Rodenburg2

12/20/21

Amplification cut off points

Hi Matthew, Amplifications are often calculated using the GISTIC algorithm. See the GISTIC

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Amplification cut off points

Hi Matthew, Amplifications are often calculated using the GISTIC algorithm. See the GISTIC

12/20/21

Jamie O'CONNOR, Benjamin Gross2

12/17/21

Keycloak and cBioportal

Hi Jamie, For starters, I think you need to instruct the web-app runner that there is a proxy server

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Keycloak and cBioportal

Hi Jamie, For starters, I think you need to instruct the web-app runner that there is a proxy server

12/17/21

Stuckel, Alexei, David Higgins2

12/16/21

TCGA FPKM and Beta values for colon cancer vs controls

Hello Alexei, Thank you for your kind words, we're glad to hear cBioPortal has been useful in

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TCGA FPKM and Beta values for colon cancer vs controls

Hello Alexei, Thank you for your kind words, we're glad to hear cBioPortal has been useful in

12/16/21

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