add_multifreq           Add multi-letter information to a motif.
ArabidopsisMotif        Arabidopsis motif in 'universalmotif' format.
ArabidopsisPromoters    Arabidopsis promoters as a 'DNAStringSet'.
compare_motifs          Compare motifs.
compare_motifs2         Faster minimalist motif comparison.
convert_motifs          Convert motif class.
convert_type            Convert universalmotif type.
create_motif            Create a motif.
create_sequences        Create random sequences.
dedup_hits              Deduplicate overlapping motif hits.
enrich_motifs           Enrich for input motifs in a set of sequences.
enrich_motifs2          Fast minimalist motif enrichment.
examplemotif            Example motif in 'universalmotif' format.
examplemotif2           Another example motif in 'universalmotif'
                        format.
filter_motifs           Filter a list of motifs.
fontDFroboto            Polygon coordinates for plotting letters.
get_bkg                 Calculate sequence background.
implant_motifs          Implant sampled motif instances into sequences
                        at known positions.
JASPAR2018_CORE_DBSCORES
                        JASPAR2018 CORE database scores
make_DBscores           Create P-value databases.
match_bkg               Sample composition-matched background sequences
                        from a universe.
merge_motifs            Merge motifs.
merge_motifs2           Merge a list of motifs into a single consensus
                        motif.
merge_similar           Identify and merge similar motifs within a
                        collection of motifs (or simply cluster
                        motifs).
merge_similar2          Cluster similar motifs by significance and
                        merge each cluster.
motif_coocc             Find significantly co-occurring motif pairs in
                        a set of sequences.
motif_finder            Discover _de novo_ motifs in a set of
                        sequences.
motif_peaks             CentriMo-style positional enrichment of motif
                        hits.
motif_pvalue            Motif P-value and scoring utility
motif_rc                Get the reverse complement of a DNA or RNA
                        motif.
motif_tree              Generate 'ggplot2' motif trees with 'ggtree'.
motif_tree2             Generate ggtree-based motif trees using
                        'compare_motifs2()'.
plot_match_bkg          Visualise composition match between target and
                        background sequences.
plot_motif_peaks        Plot the position distribution of motif hits.
read_cisbp              Import CIS-BP motifs.
read_homer              Import HOMER motifs.
read_jaspar             Import JASPAR motifs.
read_matrix             Import motifs from raw matrices.
read_meme               Import MEME motifs.
read_motifs             Import universalmotif formatted motifs.
read_transfac           Import TRANSFAC motifs.
read_uniprobe           Import UNIPROBE motifs.
run_meme                Run MEME from within R.
sample_sites            Generate binding sites from a motif.
scan_sequences          Scan sequences for matches to input motifs.
scan_sequences2         Minimalist motif scanner aligned with yamtk
                        scan defaults.
sequence_complexity     Calculate sequence complexity.
shuffle_motifs          Shuffle motifs by column.
shuffle_sequences       Shuffle input sequences.
switch_alph             Switch between DNA and RNA alphabets.
tidy-motifs             Tidy manipulation of motifs.
trim_cwm                Trim CWM motifs by absolute column sum.
trim_motifs             Trim motifs.
universalmotif-class    universalmotif: Motif class.
universalmotif-pkg      universalmotif: Import, Modify and Export
                        Motifs with R
utilities               Utility functions.
utils-motif             Motif-related utility functions.
utils-sequence          Sequence-related utility functions.
view_logo               Plot logos from numeric matrices.
view_motifs             Plot motif logos.
view_motifs2            Plot motif logos using 'compare_motifs2()'
                        alignment (v2).
write_homer             Export motifs in HOMER format.
write_jaspar            Export motifs in JASPAR format.
write_matrix            Export motifs as raw matrices.
write_meme              Export motifs in MEME format.
write_motifs            Export motifs in universalmotif format.
write_transfac          Export motifs in TRANSFAC format.
