Install lisaR

You need R 4.1 or later and internet access. RStudio is optional. If you only want to read an existing HTML report, you do not need R.

Install the package

Run this once in R or the RStudio Console:

install.packages(c("BiocManager", "remotes"))
BiocManager::install("fgsea", update = FALSE, ask = FALSE)
remotes::install_github(
  "DBM-OlmedaLab/lisaR",
  upgrade = "never",
  build_vignettes = FALSE
)

library(lisaR)
packageVersion("lisaR")

The installer brings in the required dependencies, including hommel. lisaR includes its LISA dictionaries and category hierarchy. There is no second source-file installation.

The external gene-set membership resource is prepared in the next step, alongside the Riaz data. You do not need to locate those files yourself.

If installation fails

Restart R if an older lisaR version is already loaded. For a missing dependency, compiler requirement or library-path problem, see Installation details.

The guides are available online; building HTML vignettes is not required to run an analysis. Source .Rmd files remain in the repository’s vignettes/ directory.

Next: Run Riaz ON.