enrich_TF_ChEA3_genes: Find the TF that are enriched in the differential genes using...

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Find the TF that are enriched in the differential genes using ChEA3 API

Description

Find the TF that are enriched in the differential genes using ChEA3 API

Usage

enrich_TF_ChEA3_genes(genes)

Arguments

genes

A character vector with the name of genes to enrich for TF.

Value

Returns a SingleCellExperiment object containing list of enriched Gene Sets for each cluster, either in depleted features, enriched features or simply differential features (both).

References

Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz M, Utti V, Jagodnik K, Kropiwnicki E, Wang Z, Ma'ayan A (2019) ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Research. doi: 10.1093/nar/gkz446 +

Examples

data(scExp)
enrich_TF_ChEA3_genes(head(unlist(strsplit(SummarizedExperiment::rowData(scExp)$Gene, split = ",", fixed = TRUE)), 15))

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.