Introduction

EnrichR (Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44(W1):W90-W97. and Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).) is a GSE (Gene Set Enrichment) method that infers biological knowledge by performing enrichment of input gene sets with curated biologically relevant prior databases that represent biological functions or functional pathways. The singleCellTK offers an easy to use interface to the EnrichR method and only requires the selection of input genes and the databases against which the genes should be tested.

General Worflow

The figure below describes the workflow of using EnrichR through singleCellTK console interface:

Workflow Guide

An overall workflow guide on how to use EnrichR is described below.

  1. Select genes and databases:
genes <- c("HES1", "PON2", "FBXO44", "DEK", "SOX4", "FBXL16")
databases <- enrichR::listEnrichrDbs()$libraryName
  1. Run enrichR:
enrichRes <- enrichRSCE(inSCE = sce,
                        glist = genes,
                        db = databases)
  1. Display results:
print(enrichRes)