queryChEA3: Query ChEA3 API for TF enrichment

In rChEA3: R Client for the 'ChEA3' Transcription Factor Enrichment API

Query ChEA3 API for TF enrichment

Description

#' Sends a gene list to the ChEA3 web service to identify enriched transcription factors using multiple evidence sources. The gene list should consist of HGNC-approved gene symbols.

Usage

queryChEA3(genes, query_name = "rChEA3_query", verbose = TRUE)

Arguments

genes	Character vector of HGNC gene symbols.
query_name	Optional query name (default: "rChEA3_query").
verbose	Logical; if TRUE, print a grouped summary of available result collections (default: TRUE).

Value

A named list of data frames. Each element corresponds to a ChEA3 collection and contains an enrichment table with transcription factors and their statistics. The expected names are: c("Integrated–meanRank", "Integrated–topRank", "GTEx–Coexpression", "ARCHS4–Coexpression", "ENCODE–ChIP-seq", "ReMap–ChIP-seq", "Literature–ChIP-seq", "Enrichr–Queries").

Examples

    results <- queryChEA3(c("SMAD9","FOXO1","MYC","STAT1","STAT3","SMAD3"))
    names(results)
    head(results[["Integrated--meanRank"]])

rChEA3 documentation built on Nov. 5, 2025, 6:49 p.m.