Seeking Tutorial for Downloading TCGA Data with TCGAbiolinks and Converting to TPM
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.
• 2,950 views
•
link
updated
by
Ming Tommy Tang
•
written
by
Znow •
•
written
by
Znow •
1 answer
There are step by step tutorials available on their Bioconductor page: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html
Log in to answer this question.
More posts like this
-
TCGAbiolinks: Accessing Matched Samples' Data Across -Omics Hierarchies
written by Desmond •
-
Am I getting TPM correct from tcga?
written by Znow •
-
TPM RNA-seq data for differential expression analysis
written by Catalin-George •
-
Using TCGABioLinks to query multiple cancer studies
written by ivykosater •
-
Can I use Negative Binomial regression to model TPM counts?
written by guillepalou4 •
-
Manually logging TPM count matrix in Seurat
written by ww22runner •
-
retrieve TPM matrix from raw counts matrix or DESeq2 object dds
written by StartR •
-
problem for 2 different normalization methods in train and test data set
written by modarzi
-
Percent Relative Abundance to TPM | RNA-Seq
written by G.S •
-
Converting TCGA expression data from FPKM to TPM
written by Alex Reynolds
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/