Package index
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CTCF_ChIP_peaks - Example ChIP-seq peak file
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CTCF_TIP_peaks - Example TIP-seq peak file
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MotifPeeker() - Benchmark epigenomic profiling methods using motif enrichment
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bpapply() - Use BiocParallel functions with appropriate parameters
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calc_frip() - Calculate FRiP score
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check_ENCODE() - Check for ENCODE input
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check_JASPAR() - Check for JASPAR input
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check_genome_build() - Check genome build
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denovo_motifs() - Find de-novo motifs in sequences
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find_motifs() - Find similar motifs
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format_exptype() - Format exp_type
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get_JASPARCORE() - Download JASPAR CORE database
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get_df_distances() - Get dataframe with motif-summit distances
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get_df_enrichment() - Get dataframe with motif enrichment values
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motif_MA1102.3 - Example CTCFL JASPAR motif file
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motif_MA1930.2 - Example CTCF JASPAR motif file
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motif_enrichment() - Calculate motif enrichment in a set of sequences
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motif_similarity() - Compare motifs from segregated sequences
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plot_enrichment_individual() - Plot motif-enrichment for individual experiments
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plot_enrichment_overall() - Plot motif-enrichment for all experiments
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pretty_number() - Convert numbers to more readable strings
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read_motif_file() - Read a motif file
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read_peak_file() - Read MACS2/3 narrowPeak or SEACR BED peak file
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report_command() - Report command
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report_header() - Report header
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save_peak_file() - Minimally save a peak object to a file (BED4)
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segregate_seqs() - Segregate input sequences into common and unique groups
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summit_to_motif() - Calculate the distance between peak summits and motifs
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to_plotly() - Convert ggplot2 objects to plotly
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trim_seqs() - Trim sequences to a specified width around the summit