How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types

Sign up for my newsletter to not miss a post like this The Cancer Genome Atlas (TCGA) project is probably one of the most well-known large-scale cancer sequencing project. It sequenced ~10,000 treatment-naive tumors across 33 cancer types. Different data including whole-exome, whole-genome, copy-number (SNP array), bulk RNAseq, protein expression (Reverse-Phase Protein Array), DNA methylation are available. TCGA is a very successful large sequencing project. I highly recommend learning from the organization of it.