monaLisa is a collection of tools that simplify motif enrichment analyses in genomic regions of interest.
She makes use of her father Homer (http://homer.ucsd.edu/homer/index.html) and other algorithms to search for motif hits and look for enriched motifs in sets of genomic regions, compared to all other regions.
Known motifs can for example be obtained from a collection of transcription factor binding site specificities, such as JASPAR2020.