Perform enrichment analysis for eRegulon genes against gene ontology (GO) terms and KEGG pathways

Source: R/run_stream.R

This function aims to calculate the enrichment of genes in each eRegulon against gene ontology (GO) terms or KEGG pathways. Finally, this function returns a list of data.frame objects, each of which represents one functional genomics databases, e.g., Biological Process, Molecular Function, Cellular Component, and KEGG pathways (human or mouse).

enrich_genes(regs = NULL, dbs = c("GO", "KEGG"), org = "human")

Arguments

regs

The list of enhancer regulons (eRegulons) or cell-type-specific eRegulons.

dbs

The list of databases to run enrichment analysis, c("GO", "KEGG") by default.

org

The organism, "human" by default.

References

Li, Y., Ma, A., Wang, Y., Wang, C., Chen, S., Fu, H., Liu, B. and Ma, Q., 2022. Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. bioRxiv, pp.2022-12.

Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., ... & Ma'ayan, A. (2016). Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic acids research, 44(W1), W90-W97.