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FireBrowse

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Suggested by: Roy Granit

Description

FireBrowse is a tool that provides simple and elegant means to explore TCGA cancer data, using by a powerful computational infrastructure, application programming interface (API), graphical tools and online reports. Firebrowse sits above the TCGA GDAC Firehose, one of the deepest and most integratively characterized open cancer datasets in the world--with over 80K sample aliquots from 11,000+ cancer patients, spanning 38 unique disease cohorts. FireBrowse makes it possible to find any of thousands of data archives generated by Firehose in just 2 clicks. Likewise, two clicks are all that's needed to find any of the ~1500 analysis reports created by Firehose in each analysis run. For programmers a powerful RESTful API is provided, with bindings to the UNIX command line, Python and R. And for scientists we provide graphical tools like viewGene to explore expression levels, and iCoMut to explore the comprehensive analysis profile of each TCGA disease study within a single, interactive figure.

Discussion

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Aurel Anzinger

Undergraduate at Ludwig Maximilian University of Munich

Comparison of TCGA (cancer Data) to healthy tissue using firebrowse Oval 17

Hi there!
Is there the possiblity to compare TCGA Data with Data of healthy tissue using FireBrowse, like XenaBrowser does it with the TCGA Dataset and the one of GTex? If so, how? I have seen the function, where you can plot the expression of certain genes, in the resulting graph normal tissue is shown aswell, but where does the data derive from?

I´m a total new to this field since i´ve just recently got involved into a bioinformatics project! I was already looking at various Tutorials , but I haven´t found the answer for that question yet? So mabye someone is able to answer that question!

Thanks in Advance
Best,
Aurel

upvotecomment_icon_normal 2 upvotes 1 comments Reply
Posted: 1 month ago

Ron Rotkopf

Staff member at Weizmann Institute

The best way to work with this data is to download it, and then you're free to use any software you like. For instance, you can download the clinical data and the mRNA data for a certain cohort as separate files, merge them and go on from there. If you just want to compare primary tumor to healthy tissue, note that in TCGA, the barcode for primary tumor is "01", and for healthy tissue it is "11".

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Posted: 1 month ago
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Associated keywords

Database Gene Expression Cancer

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