Isoform level TCGA RNA-seq Expression data

Question

[deepak18]

I have Isoform level RNA-seq data from The Cancer Genome Atlas and I want to check the difference the difference in the level of a particular isoform between cancer and normal samples. Is there any software or R package which I can use to plot a boxplot showing difference in that isoform between normal and cancer sample with p-value?

[hofman.bartlomiej]

If I may ask, how did you obtain Isoform level RNA-seq data from TCGA? I am trying to do so via TCGAbiolinks R package, however, without positive results

Answer 1

[igor]

You can try ggpubr.

Example plot: