# Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

## Documentation for package ‘MotifPeeker’ version 1.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

bootstrap_distances | Bootstrap motif-summit distances for one set of peaks and one motif
calc_frip | Calculate FRiP score
check_ENCODE | Check for ENCODE input
check_genome_build | Check genome build
check_JASPAR | Check for JASPAR input
CTCF_ChIP_peaks | Example ChIP-seq peak file
CTCF_TIP_peaks | Example TIP-seq peak file
denovo_motifs | Discover motifs in sequences
find_motifs | Find similar motifs
get_df_distances | Get dataframe with motif-summit distances
get_df_distances_bootstrapped | Get dataframe with bootstrapped motif-summit distances
get_df_enrichment | Get dataframe with motif enrichment values
get_JASPARCORE | Download JASPAR CORE database
MotifPeeker | Benchmark epigenomic profiling methods using motif enrichment
motif_enrichment | Calculate motif enrichment in a set of sequences
motif_MA1102.3 | Example CTCFL JASPAR motif file
motif_MA1930.2 | Example CTCF JASPAR motif file
motif_similarity | Compare motifs from segregated sequences
read_motif_file | Read a motif file
read_peak_file | Read MACS2/3 narrowPeak or SEACR BED peak file
save_peak_file | Minimally save a peak object to a file (BED4)
segregate_seqs | Segregate input sequences into common and unique groups
summit_to_motif | Calculate the distance between peak summits and motifs