Preparation

Here are some preparation information for the participants.

Software

In this workshop we will be using R. You can either

  • have R and Rstudio installed on your laptop
  • or, use Posit cloud (formerly Rstudio Cloud).

Posit cloud is free of charge for personal users, yet you need to sign up for a new user account and have internet connection.

Install Bioconductor

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.17")

Install Bioconductor Packages

BiocManager::install(c("TCGAbiolinks", "SummarizedExperiment", "maftools"))

Data

The datasets we use can be found here Genomic Data Commons (GDC): https://gdc.cancer.gov/.

Code

The R scripts used in part 1 and part 2 can be found here https://github.com/omicscenter/TCGADataAnalysiswithR.