Setup

Please follow the instructions in Workshop Materials to download the files.

It is essential you have R and RStudio installed, and please bring your own laptop for the workshop.

Please make sure all packages are installed prior to the workshop.

Install/update BiocManager to version 3.18.

install.packages("BiocManager") 
BiocManager::install(version = "3.18")

Then install the packages.

BiocManager::install("SPIAT") 
BiocManager::install("spaSim")

And these packages:

install.packages(c("elsa", "Rtsne", "umap", "alphahull", "plotly", "survminer", 
                   "survival", "vroom", "rmarkdown", "knitr"))
BiocManager::install("ComplexHeatmap")

If asked to update all/some/none packages, please answer with a.

If asked to install the compilation packages, please answer with Yes.

Note: If you don’t want to change your current library, it’s better to create a new R project and use the package renv (https://rstudio.github.io/renv/articles/renv.html) to install the packages for this workshop.

Please email yuzhou.feng@petermac.org if you have any issue installing the packages.