Skip to contents

All functions

CTCF_ChIP_peaks
Example ChIP-seq peak file
CTCF_TIP_peaks
Example TIP-seq peak file
MotifPeeker()
Benchmark epigenomic profiling methods using motif enrichment
calc_frip()
Calculate FRiP score
check_ENCODE()
Check for ENCODE input
check_JASPAR()
Check for JASPAR input
check_genome_build()
Check genome build
denovo_motifs()
Find de-novo motifs in sequences
find_motifs()
Find similar motifs
get_JASPARCORE()
Download JASPAR CORE database
get_df_distances()
Get dataframe with motif-summit distances
get_df_enrichment()
Get dataframe with motif enrichment values
motif_MA1102.3
Example CTCFL JASPAR motif file
motif_MA1930.2
Example CTCF JASPAR motif file
motif_enrichment()
Calculate motif enrichment in a set of sequences
motif_similarity()
Compare motifs from segregated sequences
plot_enrichment_overall()
Plot motif-enrichment for all experiments
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