Reference

Core Tools
runStreme()	Denovo motif discovery of target regions using STREME
runDreme()	Denovo motif discovery of target regions using DREME
runMeme()	Identify motifs with MEME
runTomTom()	Run TomTom on target motifs
runAme()	Motif enrichment using AME
runFimo()	Find instances of motifs using FIMO
Utilities
check_meme_install()	Check user's MEME install
meme_is_installed()	Returns logical vector indicating valid MEME-Suite install status
get_sequence()	Get sequence from GRanges
add_sequence()	Add nucleic acid sequence of regions to metadata column
write_fasta()	Write fasta file from stringset
Data Visualization
view_tomtom_hits()	Compare top tomtom hits to original motif
plot_sequence_heatmap()	Visualize a heatmap of aligned sequences
plot_ame_heatmap()	Plot AME heatmap clustered by similarity in detected motifs
ame_compare_heatmap_methods()	Compare AME heatmap methods
Motif Manipulation
remove_duplicate_motifs()	Remove duplicated motif entries
has_duplicate_motifs()	Check for duplicated motif matrices
Data Helpers
force_best_match()	Force best tomtom match by id
update_best_match()	Update best match info by ranking of tomtom data
drop_best_match()	Drop best match columns from tomtom results
nest_tomtom()	Nest TomTom results columns into a data.frame column named "tomtom"
Data Import
importStremeXML()	Import Streme output from previous run
importDremeXML()	Import Dreme output from previous run
importTomTomXML()	Import tomtom data from previous run
importAme()	Parse AME output
importFimo()	Import FIMO results
importMeme()	Import MEME results
Example Datasets
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