Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

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Documentation for package ‘MotifPeeker’ version 1.1.1

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

Help Pages

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_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