Appendix A — Setup

A.1 Software

  1. R. If you don’t have R installed, download and install it from CRAN.
  2. RStudio. Download and install it from RStudio’s website.
  3. R packages. Install the following packages by running the following code in RStudio:
# Needed for most chapters
install.packages("tidyverse")

# Needed for certain chapter
install.packages(c("plotly",
                   "DT",
                   "knitr",
                   "rmarkdown",
                   "survminer",
                   "ModelMetrics",
                   "gower",
                   "randomForest",
                   "gbm",
                   "glmnet",
                   "mice",
                   "prophet",
                   "tidytext",
                   "gutenbergr",
                   "tm",
                   "topicmodels"))

# For the predictive modeling chapter
install.packages("caret", dependencies = c("Depends", "Suggests"))

# Bioconductor packages are installed differently
install.packages("BiocManager")
BiocManager::install(c("DESeq2", 
                       "RTCGA", 
                       "RTCGA.clinical", 
                       "RTCGA.mRNA", 
                       "ggtree", 
                     "Biostrings"))

A.2 Data

  1. Option 1: Download all the data. Download and extract this zip file (11.36 Mb) with all the data for the entire workshop. This may include additional datasets that we won’t use here.
  2. Option 2: Download individual datasets as needed.
    • Create a new folder somewhere on your computer that’s easy to get to (e.g., your Desktop). Name it bds. Inside that folder, make a folder called data, all lowercase.
    • Download individual data files as needed, saving them to the new bdsr/data folder you just made. Click to download. If data displays in your browser, right-click and select Save link as… (or similar) to save to the desired location.