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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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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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_overall()
- Plot motif-enrichment for all experiments
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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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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