# motif matching, comparison, and de novo discovery using the MEME Suite

## Documentation for package ‘memes’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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