cBioPortal for Cancer Genomics Discussion Group

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Arushi Rai, Priti Kumari2

Oct 14

MRNA Z scores QUERY

Hi Arushi, You can download the raw data from datahub: https://github.com/cBioPortal/datahub/tree/

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MRNA Z scores QUERY

Hi Arushi, You can download the raw data from datahub: https://github.com/cBioPortal/datahub/tree/

Oct 14

Oct 14

Mutational signature in GDC HGSOC Dataset

To whom it may concern, I am contacting you for the following reason: I'm doing my thesis using

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Mutational signature in GDC HGSOC Dataset

To whom it may concern, I am contacting you for the following reason: I'm doing my thesis using

Oct 14

Boeschen, Myriam, Priti Kumari3

Oct 14

cBioPortal user reported error

Hi Myriam, The following URL should work: https://www.cbioportal.org/results/comparison?

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cBioPortal user reported error

Hi Myriam, The following URL should work: https://www.cbioportal.org/results/comparison?

Oct 14

Joseph Celidonio, … de Bruijn, Ino24

Oct 14

Variable Definition Confirmation

Good morning, I hope you all had a great weekend. I want to thank you for providing your guidance on

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Variable Definition Confirmation

Good morning, I hope you all had a great weekend. I want to thank you for providing your guidance on

Oct 14

niels bohr, Aaron L2

Oct 11

previous issue already solved!!!

glad to hear it! and thank you for your tremendous contribution to quantum physics! On Fri, Oct 11,

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previous issue already solved!!!

glad to hear it! and thank you for your tremendous contribution to quantum physics! On Fri, Oct 11,

Oct 11

Oct 11

download the mRNA z scores (RAW DATA)

Arushi Rai <rai...@udayton.edu>Hello, I have these four sample patient IDs that I extracted

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download the mRNA z scores (RAW DATA)

Arushi Rai <rai...@udayton.edu>Hello, I have these four sample patient IDs that I extracted

Oct 11

内田士朗, … Benjamin Gross6

Oct 11

Inquiry Regarding Age-specific Analysis in cBioPortal for Breast Cancer Studies

Dear Sir/Madam, Thank you for your response. I understand that it is possible to divide the age

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Inquiry Regarding Age-specific Analysis in cBioPortal for Breast Cancer Studies

Dear Sir/Madam, Thank you for your response. I understand that it is possible to divide the age

Oct 11

Bosc L, … Fabian Ortega3

Oct 11

Download lower level copy number alterations from cBioPortal

Is there information about how these cna files were aggregated? I was trying to do a mass download of

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Download lower level copy number alterations from cBioPortal

Is there information about how these cna files were aggregated? I was trying to do a mass download of

Oct 11

Oct 11

Access denied for user 'cbio_user'

Hi everyone, i ran your simple quick start guide (so pull, init, and docker compose up) but the

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Access denied for user 'cbio_user'

Hi everyone, i ran your simple quick start guide (so pull, init, and docker compose up) but the

Oct 11

Cayetano Galera Martinez, Priti Kumari3

Oct 10

Hi Priti, Everything solved! Thanks! Best, Caye Enviado desde Outlook para iOS De: Priti Kumari <

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Hi Priti, Everything solved! Thanks! Best, Caye Enviado desde Outlook para iOS De: Priti Kumari <

Oct 10

Shain, Alan Hunter, … Ritika Kundra3

Oct 9

Deposition of somatic mutation data from phenotypically normal cells

Hi Hunter, Thank you for reaching out to us. We will contact you separately to set this up. Thanks,

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Deposition of somatic mutation data from phenotypically normal cells

Hi Hunter, Thank you for reaching out to us. We will contact you separately to set this up. Thanks,

Oct 9

scientist simon, Benjamin Gross2

Oct 8

Question about TCGA data usage policy

Hi Sahoon, It looks like the data usage policy link on gdac.broadinstitute.org is no longer working.

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Question about TCGA data usage policy

Hi Sahoon, It looks like the data usage policy link on gdac.broadinstitute.org is no longer working.

Oct 8

Sergi Aguiló-Castillo, Benjamin Gross3

Oct 8

Import Studies Example not working

Hi Sergi, Thank you for your report. I've created an issue in our bug tracker so that a

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Import Studies Example not working

Hi Sergi, Thank you for your report. I've created an issue in our bug tracker so that a

Oct 8

Dennis Moccia, Benjamin Gross2

Oct 7

Cancer Types Summary and API

Hi Dennis, I loaded a cancer types summary page/tab with the chrome browser dev tool network tab open

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Cancer Types Summary and API

Hi Dennis, I loaded a cancer types summary page/tab with the chrome browser dev tool network tab open

Oct 7

Efstathios Vlachavas, Benjamin Gross2

Oct 7

License terms and restrictions querying and downloading specific datasets through the cBioPortal web portal

Hi Efstathios, The AGPL license pertains to the cBioPortal source code, not the data. I believe most

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License terms and restrictions querying and downloading specific datasets through the cBioPortal web portal

Hi Efstathios, The AGPL license pertains to the cBioPortal source code, not the data. I believe most

Oct 7

aghil hooshmand, Trevor Pugh2

Oct 3

Teaching cbioportal through case studies with a focus on multi-omics integration.

Hi Aghil, You may be interested in our collection of Tutorials, Webinars, and How To Videos here:

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Teaching cbioportal through case studies with a focus on multi-omics integration.

Hi Aghil, You may be interested in our collection of Tutorials, Webinars, and How To Videos here:

Oct 3

Sergio Alvarez, jagn...@gmail.com2

Oct 2

Hi Sergio, It is possible to create groups such as before and after treatment. For that the samples

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Hi Sergio, It is possible to create groups such as before and after treatment. For that the samples

Oct 2

Atul Anand, Benjamin Gross2

Oct 2

Hi Atul, Please provide the original query/URL you are attempting to make within the GENIE portal

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Hi Atul, Please provide the original query/URL you are attempting to make within the GENIE portal

Oct 2

Oct 2

Dear Cbioportal AACR Genie Team, I am getting below error can you please help me?

"{\"req\":{\"method\":\"POST\",\"url\":\"//genie.

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Dear Cbioportal AACR Genie Team, I am getting below error can you please help me?

"{\"req\":{\"method\":\"POST\",\"url\":\"//genie.

Oct 2

Thomas Pauli, jagn...@gmail.com9

Oct 2

api/session/* endpoints - Internal Server Error

Hi Jag, I actually don't know where the password that was displayed in the log came from. I haven

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api/session/* endpoints - Internal Server Error

Hi Jag, I actually don't know where the password that was displayed in the log came from. I haven

Oct 2

Lomibao, Meghanne, … Trevor Pugh4

Oct 1

Cbioportal Questions-Help Needed

Hi Meghanne, Here are some answers to your questions 1. We are collecting tumor fraction values. Are

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Cbioportal Questions-Help Needed

Hi Meghanne, Here are some answers to your questions 1. We are collecting tumor fraction values. Are

Oct 1

Panagiotis Fotakis, jagn...@gmail.com2

Sep 30

question on error bars when plotting the data by RNA expression

Hi Panagiotis, The Plots tab shows a standard box and whiskers plot. I am assuming the whiskers are

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question on error bars when plotting the data by RNA expression

Hi Panagiotis, The Plots tab shows a standard box and whiskers plot. I am assuming the whiskers are

Sep 30

Li, Guangyuan, … Federico Vannuccini6

Sep 29

Inquiry about mRNA expression values

Dear Li Guangyuan, I'm sharing a Dropbox link to an .rda file containing the FPKM data without z-

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Inquiry about mRNA expression values

Dear Li Guangyuan, I'm sharing a Dropbox link to an .rda file containing the FPKM data without z-

Sep 29

Joris Vos, jagn...@gmail.com3

Sep 28

IMPACT panel sizes

Hi Jag, Thanks! That's very helpful. Have a great day, Joris On Friday, September 27, 2024 at 11:

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IMPACT panel sizes

Hi Jag, Thanks! That's very helpful. Have a great day, Joris On Friday, September 27, 2024 at 11:

Sep 28

SHI, YUFEI, … Schultz, Nikolaus12

Sep 27

RE: Reminder# cBioportal# OS for (Col6a3) by using cBioportal & KM plotter

Hi Yufei, The four different TCGA thyroid cancer data sets reflect slightly different versions and

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RE: Reminder# cBioportal# OS for (Col6a3) by using cBioportal & KM plotter

Hi Yufei, The four different TCGA thyroid cancer data sets reflect slightly different versions and

Sep 27

Aaron Atkinson, Aaron L2

Sep 26

Clinical Track Ordering

Hi Aaron (from a fellow Aaron) Can you send me the response for this request on your portal (with

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Clinical Track Ordering

Hi Aaron (from a fellow Aaron) Can you send me the response for this request on your portal (with

Sep 26

Slman s29, jagn...@gmail.com2

Sep 26

Hi, It is possible to create a combined study of all the datasets that you are interested. After that

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Hi, It is possible to create a combined study of all the datasets that you are interested. After that

Sep 26

Giulia Mantini, jagn...@gmail.com2

Sep 26

PDAC MSK data 2024

Hi Giulia We are in the process of uploading the entire study dataset to our portal. I will keep you

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PDAC MSK data 2024

Hi Giulia We are in the process of uploading the entire study dataset to our portal. I will keep you

Sep 26

Yahya Daneshbod, Aaron L2

Sep 26

Can you try this again? If it reoccurs, please let us know the sets that you took prior to make the

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Can you try this again? If it reoccurs, please let us know the sets that you took prior to make the

Sep 26

Abhishek Reddy, jagn...@gmail.com2

Sep 26

HTTPS and OKTA or KeyCloak

HI Abhishek, To enable HTTPS, we need to route the port 443 to port 80 (or other cBioPortal port). A

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HTTPS and OKTA or KeyCloak

HI Abhishek, To enable HTTPS, we need to route the port 443 to port 80 (or other cBioPortal port). A

Sep 26

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