Assembled TCGA dataset download
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8.5 years ago
Pappu ★ 2.1k

I am looking for assembled TCGA dataset with listed somatic mutations, copy number variations, epigenetic modifications etc. I am wondering if there is any resource with all the basic analysis done.

TCGA • 2.7k views
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8.5 years ago
Amitm ★ 2.3k

hi, Have you heard of the cBioPortal website. It has I think most of the TCGA cancer cohorts analyzed for mutations, copy number and expression. Its here - http://www.cbioportal.org/

Not everything that can be done with somatic mut./ CNA/ RNA-seq data, is present here, but its a good a online resource could be for testing hypothesis and finding recurrent patterns without getting in muddy waters of analyzing oneself.

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Just noted that 'downloaded' was mentioned in the question. So clarifying that cBioPortal wont allow download of 'whole' datasets in one go. But you could query a max. of 100 genes in parallel. But it still is a very good resource.

Another resource is this - http://bioinformatics.mdanderson.org/tcgambatch/ You dont get digested results (like recurring mut./ CNA etc.) here, but you can download batch-effect corrected 'whole' datasets from here. The exclusive advantage of this resource is that you get all data types available (like methylation, rppa etc. which aren't available on cBioPortal I think) here.

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8.5 years ago
ivivek_ngs ★ 5.2k

You can download in batch from specific cancer type using TCGA Assembler . They provide an excellent resource manual.You can also take a look at this enter link description here . They offer visualisation as well and easy toggle download button. Or you can download data from Firebrowse using firehose_get script. There is a new paper which states downloaded data can be directly processed ut I have not read the entire paper , you can take a look however I did not find the web link of the platform.

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