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| get_genomic_annotations | Annotate genomic regions |
| get_variable_regions | Get variable regions |
| merge_GR | Merge genomic regions |
| multiBigwig_summary | Enrichments at genomics regions |
| plot_browser_tracks | UCSC Genome browser like plots |
| plot_correlation | Correlations among replicates/groups |
| plot_enrichments | Enrichment plots |
| plot_genomic_annotations | Plot genomic annotations |
| plot_motif_logo | Plot sequence motifs |
| process_homer | Process homer format |
| process_jaspar | Process jaspar format |
| process_meme | Process meme format |
| process_pfm | Process PFM format |
| process_transfac | Process transfac format |