Man pages for bjmt/universalmotif
Import, Modify, and Export Motifs with R

add_multifreqAdd multi-letter information to a motif.
ArabidopsisMotifArabidopsis motif in 'universalmotif' format.
ArabidopsisPromotersArabidopsis promoters as a 'DNAStringSet'.
compare_motifsCompare motifs.
convert_motifsConvert motif class.
convert_typeConvert universalmotif type.
create_motifCreate a motif.
create_sequencesCreate random sequences.
enrich_motifsEnrich for input motifs in a set of sequences.
examplemotifExample motif in 'universalmotif' format.
examplemotif2Another example motif in 'universalmotif' format.
filter_motifsFilter a list of motifs.
get_bkgCalculate sequence background.
JASPAR2018_CORE_DBSCORESJASPAR2018 CORE database scores
make_DBscoresCreate P-value databases.
merge_motifsMerge motifs.
motif_peaksLook for overrepresented motif position peaks in a set of...
motif_pvalueMotif P-value and scoring utility
motif_rcGet the reverse complement of a DNA or RNA motif.
motif_treeGenerate 'ggplot2' motif trees with 'ggtree'.
read_cisbpImport CIS-BP motifs.
read_homerImport HOMER motifs.
read_jasparImport JASPAR motifs.
read_matrixImport motifs from raw matrices.
read_memeImport MEME motifs.
read_motifsImport universalmotif formatted motifs.
read_transfacImport TRANSFAC motifs.
read_uniprobeImport UNIPROBE motifs.
reexportsObjects exported from other packages
run_memeRun MEME from within R.
sample_sitesGenerate binding sites from a motif.
scan_sequencesScan sequences for matches to input motifs.
shuffle_motifsShuffle motifs by column.
shuffle_sequencesShuffle input sequences.
switch_alphSwitch between DNA and RNA alphabets.
trim_motifsTrim motifs.
universalmotif-classuniversalmotif: Motif class.
universalmotif-pkguniversalmotif: Import, Modify and Export Motifs with R
utilitiesUtility functions.
utils-motifMotif-related utility functions.
utils-sequenceSequence-related utility functions.
view_motifsPlot motif logos.
write_homerExport motifs in HOMER format.
write_jasparExport motifs in JASPAR format.
write_matrixExport motifs as raw matrices.
write_memeExport motifs in MEME format.
write_motifsExport motifs in universalmotif format.
write_transfacExport motifs in TRANSFAC format.
bjmt/universalmotif documentation built on Nov. 7, 2019, 12:20 p.m.