README.md

Gene signature enrichment using UCell

In this repo we host code and scripts to run UCell in different settings.

• UCell_vignette_Seurat.Rmd, UCell_vignette_matrix.Rmd and UCell_vignette_TILstates.Rmd can be used to reproduce the vignettes (in .html) hosted on github.io:

  • Signature enrichment analysis with UCell
  • Using UCell with Seurat objects
  • Using UCell and Seurat to identify different T cell subtypes/states in human tumors

• UCell_figures4paper.Rmd contains the code to the reproduce the figures of the accompanying manuscript

• UCell_benchmarks.small.machines.Rmd has tips to simulate machines with smaller memory, to benchmark the method with different computational resources.

• wrapper_benchmark_UCell.R (which in turn runs run_benchmark_UCell.R) can be used to evaluate running time and peak memory for UCell or AUCell, with datasets of different size

More information at the UCell Bioconductor page and GitHub repo