setup.md

layout	title
page	Setup

It's usually recommended that course instructors provide a virtual environment with software and data available. However this page includes instructions to set up for the lessons. This should take about an hour to run, depending on the speed of your computer, your internet connection, and any packages you have installed already. You'll need to install R 4.0 or later.

The following code will download the data and install the libraries used in the current version of this lesson:

install.packages("BiocManager")
download.file(
    "https://raw.githubusercontent.com/carpentries-incubator/high-dimensional-stats-r/gh-pages/dependencies.csv",
    destfile = 'dependencies.csv'
)
table <- read.table('dependencies.csv')
BiocManager::install(table[[1]])

dir.create("data", showWarnings = FALSE)
data_files <- c(
    "cancer_expression.rds",
    "coefHorvath.rds",
    "methylation.rds",
    "scrnaseq.rds",
    "small_methylation.rds"
)
for (file in data_files) {
    download.file(
        url = file.path(
            "https://raw.githubusercontent.com/carpentries-incubator/high-dimensional-stats-r/gh-pages/data",
            file
        ),
        destfile = file.path("data", file)
    )
}

{% include links.md %}