API for snystrom/dremeR
motif matching, comparison, and de novo discovery using the MEME Suite
| Global functions | |
|---|---|
| add_sequence | Man page Source code |
| alph_parse_coords | Source code |
| ame_compare_heatmap_methods | Man page Source code |
| ame_help | Source code |
| ame_order_by_cluster | Source code |
| as_universalmotif | Source code |
| as_universalmotif_dataframe | Source code |
| attrs_to_df | Source code |
| build_sequence_as_granges | Source code |
| check_meme_install | Man page |
| combine_cols | Source code |
| cowplot_title | Source code |
| dreme_get_background_freq | Source code |
| dreme_help | Source code |
| dreme_motif_stats | Source code |
| dreme_to_pfm | Source code |
| drop_best_match | Man page Source code |
| duplicate_file | Source code |
| error_dreme_results | Source code |
| error_universalmotif_list | Source code |
| example_ame | Man page |
| example_ame_large | Man page |
| example_chip_summits | Man page |
| example_dreme | Man page |
| example_dreme_by_binding | Man page |
| example_dreme_tomtom | Man page |
| example_fimo | Man page |
| example_peaks | Man page |
| example_rnaseq | Man page |
| example_tomtom | Man page |
| force_best_match | Man page Source code |
| get_ame_coltypes | Source code |
| get_probability_matrix | Source code |
| get_sequence | Man page Source code |
| get_sequence.CompressedGRangesList | Source code |
| get_sequence.GRanges | Source code |
| get_sequence.GRangesList | Source code |
| get_sequence.GenomicRangesList | Source code |
| get_sequence.SimpleGRangesList | Source code |
| get_sequence.character | Source code |
| get_sequence.data.frame | Source code |
| get_sequence.list | Source code |
| has_duplicate_motifs | Man page Source code |
| has_duplicate_motifs.data.frame | Source code |
| has_duplicate_motifs.list | Source code |
| has_duplicate_motifs.universalmotif_df | Source code |
| identify_duplicate_motifs | Source code |
| importAme | Man page Source code |
| importAmeSequences | Source code |
| importDremeXML | Man page Source code |
| importFimo | Man page |
| importMeme | Man page Source code |
| importStremeXML | Man page Source code |
| importTomTomXML | Man page Source code |
| is_dreme_results | Source code |
| is_tomtom_results | Source code |
| is_universalmotif_dataframe | Source code |
| is_universalmotif_list | Source code |
| meme_alph_to_args | Source code |
| meme_help | Source code |
| meme_help_flags | Source code |
| meme_is_installed | Man page |
| memes | Man page |
| memes-package | Man page |
| memes_update_motifs | Source code |
| motif_input | Source code |
| motif_input.character | Source code |
| motif_input.data.frame | Source code |
| motif_input.list | Source code |
| motif_input.universalmotif | Source code |
| motif_input.universalmotif_df | Source code |
| mutate_motif | Source code |
| nest_tomtom | Man page Source code |
| new_dreme_results | Source code |
| new_tomtom_results | Source code |
| nomatch_logo | Source code |
| nomatch_matrix | Source code |
| outdir_name | Source code |
| parseDreme | Source code |
| plot_ame_heatmap | Man page Source code |
| plot_sequence_heatmap | Man page |
| prepareAmeFlags | Source code |
| prepareDremeFlags | Source code |
| prepareFimoFlags | Source code |
| prepareMemeFlags | Source code |
| prepareStremeFlags | Source code |
| print_process_stderr | Source code |
| print_process_stdout | Source code |
| process_check_error | Source code |
| rank_normalize | Source code |
| rank_tomtom_by_name | Source code |
| remove_duplicate_motifs | Man page Source code |
| remove_duplicate_motifs.data.frame | Source code |
| remove_duplicate_motifs.list | Source code |
| remove_duplicate_motifs.universalmotif_df | Source code |
| runAme | Man page Source code |
| runAme.BStringSetList | Man page Source code |
| runAme.default | Man page Source code |
| runAme.list | Man page Source code |
| runDreme | Man page Source code |
| runDreme.BStringSetList | Source code |
| runDreme.default | Source code |
| runDreme.list | Source code |
| runFimo | Man page Source code |
| runMeme | Man page Source code |
| runMeme.BStringSetList | Man page Source code |
| runMeme.default | Man page Source code |
| runMeme.list | Man page Source code |
| runStreme | Man page Source code |
| runStreme.BStringSet | Source code |
| runStreme.BStringSetList | Source code |
| runStreme.default | Source code |
| runStreme.list | Source code |
| runTomTom | Man page Source code |
| runTomTom.default | Source code |
| runTomTom.list | Source code |
| search_meme_database_path | Source code |
| search_meme_path | Source code |
| sequence_as_granges | Source code |
| sequence_input | Source code |
| sequence_input.AAStringSet | Source code |
| sequence_input.BStringSet | Source code |
| sequence_input.DNAStringSet | Source code |
| sequence_input.character | Source code |
| sequence_input_control_list | Source code |
| sequence_to_df | Source code |
| split_input_control | Source code |
| streme_help | Source code |
| streme_help_flags | Source code |
| tomtom_query_motif_dfs | Source code |
| update_best_match | Man page Source code |
| view_tomtom_hits | Man page Source code |
| view_tomtom_nomatch | Source code |
| write_fasta | Man page |
| write_meme_input_path | Source code |
| write_meme_list | Source code |
