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.
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.
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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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.