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"page": "add_multifreq", "title": "Add multi-letter information to a motif.", "topics": [ "add_multifreq" ] }, { "page": "ArabidopsisMotif", "title": "Arabidopsis motif in 'universalmotif' format.", "topics": [ "ArabidopsisMotif" ] }, { "page": "ArabidopsisPromoters", "title": "Arabidopsis promoters as a 'DNAStringSet'.", "topics": [ "ArabidopsisPromoters" ] }, { "page": "compare_motifs", "title": "Compare motifs.", "topics": [ "compare_motifs" ] }, { "page": "convert_motifs", "title": "Convert motif class.", "topics": [ "convert_motifs", "convert_motifs,AsIs-method", "convert_motifs,ICMatrix-method", "convert_motifs,list-method", "convert_motifs,matrix-method", "convert_motifs,Motif-method", "convert_motifs,MotifList-method", "convert_motifs,pcm-method", "convert_motifs,pfm-method", "convert_motifs,PFMatrix-method", "convert_motifs,PWM-method", "convert_motifs,pwm-method", "convert_motifs,PWMatrix-method", "convert_motifs,TFFMFirst-method", "convert_motifs,universalmotif-method", "convert_motifs,XMatrixList-method" ] }, { "page": "convert_type", "title": "Convert universalmotif type.", "topics": [ "convert_type" ] }, { "page": "create_motif", "title": "Create a motif.", "topics": [ "create_motif", "create_motif,AAStringSet-method", "create_motif,BStringSet-method", "create_motif,character-method", "create_motif,DNAStringSet-method", "create_motif,matrix-method", "create_motif,missing-method", "create_motif,numeric-method", "create_motif,RNAStringSet-method" ] }, { "page": "create_sequences", "title": "Create random sequences.", "topics": [ "create_sequences" ] }, { "page": "enrich_motifs", "title": "Enrich for input motifs in a set of sequences.", "topics": [ "enrich_motifs" ] }, { "page": "examplemotif", "title": "Example motif in 'universalmotif' format.", "topics": [ "examplemotif" ] }, { "page": "examplemotif2", "title": "Another example motif in 'universalmotif' format.", "topics": [ "examplemotif2" ] }, { "page": "filter_motifs", "title": "Filter a list of motifs.", "topics": [ "filter_motifs" ] }, { "page": "fontDFroboto", "title": "Polygon coordinates for plotting letters.", "topics": [ "fontDFroboto" ] }, { "page": "get_bkg", "title": "Calculate sequence background.", "topics": [ "get_bkg" ] }, { "page": "JASPAR2018_CORE_DBSCORES", "title": "JASPAR2018 CORE database scores", "topics": [ "JASPAR2018_CORE_DBSCORES" ] }, { "page": "make_DBscores", "title": "Create P-value databases.", "topics": [ "make_DBscores" ] }, { "page": "merge_motifs", "title": "Merge motifs.", "topics": [ "merge_motifs" ] }, { "page": "merge_similar", "title": "Identify and merge similar motifs within a collection of motifs (or simply cluster motifs).", "topics": [ "merge_similar" ] }, { "page": "motif_peaks", "title": "Look for overrepresented motif position peaks in a set of sequences.", "topics": [ "motif_peaks" ] }, { "page": "motif_pvalue", "title": "Motif P-value and scoring utility", "topics": [ "motif_pvalue" ] }, { "page": "motif_rc", "title": "Get the reverse complement of a DNA or RNA motif.", "topics": [ "motif_rc" ] }, { "page": "motif_tree", "title": "Generate 'ggplot2' motif trees with 'ggtree'.", "topics": [ "motif_tree" ] }, { "page": "read_cisbp", "title": "Import CIS-BP motifs.", "concept": [ "read_motifs" ], "topics": [ "read_cisbp" ] }, { "page": "read_homer", "title": "Import HOMER motifs.", "concept": [ "read_motifs" ], "topics": [ "read_homer" ] }, { "page": "read_jaspar", "title": "Import JASPAR motifs.", "concept": [ "read_motifs" ], "topics": [ "read_jaspar" ] }, { "page": "read_matrix", "title": "Import motifs from raw matrices.", "concept": [ "read_motifs" ], "topics": [ "read_matrix" ] }, { "page": "read_meme", "title": "Import MEME motifs.", "concept": [ "read_motifs" ], "topics": [ "read_meme" ] }, { "page": "read_motifs", "title": "Import universalmotif formatted motifs.", "concept": [ "read_motifs" ], "topics": [ "read_motifs" ] }, { "page": "read_transfac", "title": "Import TRANSFAC motifs.", "concept": [ "read_motifs" ], "topics": [ "read_transfac" ] }, { "page": "read_uniprobe", "title": "Import UNIPROBE motifs.", "concept": [ "read_motifs" ], "topics": [ "read_uniprobe" ] }, { "page": "run_meme", "title": "Run MEME from within R.", "topics": [ "run_meme" ] }, { "page": "sample_sites", "title": "Generate binding sites from a motif.", "topics": [ "sample_sites" ] }, { "page": "scan_sequences", "title": "Scan sequences for matches to input motifs.", "topics": [ "scan_sequences" ] }, { "page": "sequence_complexity", "title": "Calculate sequence complexity.", "topics": [ "sequence_complexity" ] }, { "page": "shuffle_motifs", "title": "Shuffle motifs by column.", "topics": [ "shuffle_motifs" ] }, { "page": "shuffle_sequences", "title": "Shuffle input sequences.", "topics": [ "shuffle_sequences" ] }, { "page": "switch_alph", "title": "Switch between DNA and RNA alphabets.", "topics": [ "switch_alph" ] }, { "page": "tidy-motifs", "title": "Tidy manipulation of motifs.", "topics": [ 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