motif matching, comparison, and de novo discovery using the MEME
Suite
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Documentation for package ‘memes’ version 1.17.0
Help Pages
| 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 | Motif enrichment using AME |
| runAme.BStringSetList | Motif enrichment using AME |
| runAme.default | Motif enrichment using AME |
| 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 |
| runMeme.BStringSetList | Identify motifs with MEME |
| runMeme.default | Identify motifs with MEME |
| runMeme.list | 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 |