add_sequence            Add nucleic acid sequence of regions to
                        metadata column
ame_compare_heatmap_methods
                        Compare AME heatmap methods
check_meme_install      Check user's MEME install
drop_best_match         Drop best match columns from tomtom results
example_ame             Example runAme() output
example_ame_large       runAme() output for example_chip_summits split
                        by binding description
example_chip_summits    Annotated Transcription Factor ChIP-seq summits
example_dreme           Example runDreme() output
example_dreme_by_binding
                        runDreme() output for example_chip_summits
                        split by binding description
example_dreme_tomtom    Example runDreme() output after passing to
                        runTomTom()
example_fimo            Example runFimo() output
example_peaks           Example ChIP-seq peaks
example_rnaseq          RNAseq data from Early and Late Drosophila
                        wings
example_tomtom          Example runTomTom() output
force_best_match        Force best tomtom match by id
get_sequence            Get sequence from GRanges
has_duplicate_motifs    Check for duplicated motif matrices
importAme               Parse AME output
importDremeXML          Import Dreme output from previous run
importFimo              Import FIMO results
importMeme              Import MEME results
importStremeXML         Import Streme output from previous run
importTomTomXML         Import tomtom data from previous run
meme_is_installed       Returns logical vector indicating valid
                        MEME-Suite install status
nest_tomtom             Nest TomTom results columns into a data.frame
                        column named "tomtom"
plot_ame_heatmap        Plot AME heatmap clustered by similarity in
                        detected motifs
plot_sequence_heatmap   Visualize a heatmap of aligned sequences
remove_duplicate_motifs
                        Remove duplicated motif entries
runAme.list             Motif enrichment using AME
runDreme                Denovo motif discovery of target regions using
                        DREME
runFimo                 Find instances of motifs using FIMO
runMeme                 Identify motifs with MEME
runStreme               Denovo motif discovery of target regions using
                        STREME
runTomTom               Run TomTom on target motifs
update_best_match       Update best match info by ranking of tomtom
                        data
view_tomtom_hits        Compare top tomtom hits to original motif
write_fasta             Write fasta file from stringset
