RcisTarget

RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Bioconductor version: 3.23 · Package version: 1.32.0

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RcisTarget")