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

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Documentation for package ‘memes’ version 1.12.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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