How to download a full matrix of gene expression HTSEQ counts from all TCGA cancer types

Question

[BIOGUY]

Is there an easy way to get a matrix containing the transcript counts for all the genes for all the patients for all the cancer types. I'm only seeing ways to download individual files on the GDC data portal.

Answer 1

[sophiespo]

You can easily download the counts and create this matrix yourself using the TCGAbiolinks package in R: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html