Seeking Tutorial for Downloading TCGA Data with TCGAbiolinks and Converting to TPM

Question

[Znow]

Hi everyone,

I'm currently working on a project where I need to download RNA-Seq data from The Cancer Genome Atlas (TCGA) using the TCGAbiolinks package in R. Additionally, I need to transform these data into Transcripts Per Million (TPM).

I would greatly appreciate it if someone could share a step-by-step tutorial or guide on how to achieve this.

[Ming Tommy Tang]

I did exactly this but with the recount package https://divingintogeneticsandgenomics.com/post/how-to-convert-raw-counts-to-tpm-for-tcga-data-and-make-a-heatmap-across-cancer-types/

Answer 1

[GenoMax]

There are step by step tutorials available on their Bioconductor page: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html

[Znow]

Thank you so much