raw count on TCGA/GDC

Question

[fp192]

How do get the RAW COUNT from TCGA/GDC for analysis in R? I only want processed data.

[Zhenyu Zhang]

For GDC data, using the browser to select HTSeq count data, of your custom cohort, download the manifest, and use gdc-client to get them all.

Answer 1

[Mike]

Broad GDAC Firehose would be easy way, have a look at below link..

https://gdac.broadinstitute.org/

[fp192]

Thank you. Taking a look at it now. I will get back with you on my findings

Answer 2

[David]

Have you taken a look at TCGAbiolinks? https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html Here is the vignette: https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html

[fp192]

Thank you I will have a look at my downloaded R packages. I previously did install several bioinformatic packages