# Import, Modify, and Export Motifs with R

## Documentation for package ‘universalmotif’ version 1.8.3

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

## Help Pages

add_gap | Motif-related utility functions.
add_multifreq | Add multi-letter information to a motif.
ArabidopsisMotif | Arabidopsis motif in 'universalmotif' format.
ArabidopsisPromoters | Arabidopsis promoters as a 'DNAStringSet'.
as.data.frame-method | universalmotif: Motif class.
cbind-method | universalmotif: Motif class.
colMeans-method | universalmotif: Motif class.
colnames-method | universalmotif: Motif class.
colSums-method | universalmotif: Motif class.
compare_columns | Motif-related utility functions.
compare_motifs | Compare motifs.
consensus_to_ppm | Motif-related utility functions.
consensus_to_ppmAA | Motif-related utility functions.
convert_motifs | Convert motif class.
convert_motifs-method | Convert motif class.
convert_type | Convert universalmotif type.
count_klets | Sequence-related utility functions.
create_motif | Create a motif.
create_motif-method | Create a motif.
create_sequences | Create random sequences.
enrich_motifs | Enrich for input motifs in a set of sequences.
examplemotif | Example motif in 'universalmotif' format.
examplemotif2 | Another example motif in 'universalmotif' format.
filter_motifs | Filter a list of motifs.
get_bkg | Calculate sequence background.
get_consensus | Motif-related utility functions.
get_consensusAA | Motif-related utility functions.
get_klets | Sequence-related utility functions.
get_matches | Motif-related utility functions.
get_scores | Motif-related utility functions.
icm_to_ppm | Motif-related utility functions.
initialize-method | universalmotif: Motif class.
JASPAR2018_CORE_DBSCORES | JASPAR2018 CORE database scores
log_string_pval | Motif-related utility functions.
make_DBscores | Create P-value databases.
mask_seqs | Sequence-related utility functions.
merge_motifs | Merge motifs.
motif_peaks | Look for overrepresented motif position peaks in a set of sequences.
motif_pvalue | Motif P-value and scoring utility
motif_rc | Get the reverse complement of a DNA or RNA motif.
motif_score | Motif-related utility functions.
motif_tree | Generate 'ggplot2' motif trees with 'ggtree'.
ncol-method | universalmotif: Motif class.
normalize-method | universalmotif: Motif class.
nrow-method | universalmotif: Motif class.
pcm_to_ppm | Motif-related utility functions.
position_icscore | Motif-related utility functions.
ppm_to_icm | Motif-related utility functions.
ppm_to_pcm | Motif-related utility functions.
ppm_to_pwm | Motif-related utility functions.
prob_match | Motif-related utility functions.
prob_match_bkg | Motif-related utility functions.
pwm_to_ppm | Motif-related utility functions.
read_cisbp | Import CIS-BP motifs.
read_homer | Import HOMER motifs.
read_jaspar | Import JASPAR motifs.
read_matrix | Import motifs from raw matrices.
read_meme | Import MEME motifs.
read_motifs | Import universalmotif formatted motifs.
read_transfac | Import TRANSFAC motifs.
read_uniprobe | Import UNIPROBE motifs.
round_motif | Motif-related utility functions.
rowMeans-method | universalmotif: Motif class.
rownames-method | universalmotif: Motif class.
rowSums-method | universalmotif: Motif class.
run_meme | Run MEME from within R.
sample_sites | Generate binding sites from a motif.
scan_sequences | Scan sequences for matches to input motifs.
score_match | Motif-related utility functions.
show-method | universalmotif: Motif class.
shuffle_motifs | Shuffle motifs by column.
shuffle_sequences | Shuffle input sequences.
shuffle_string | Sequence-related utility functions.
subset-method | universalmotif: Motif class.
summarise_motifs | Motif-related utility functions.
switch_alph | Switch between DNA and RNA alphabets.
trim_motifs | Trim motifs.
ungap | Motif-related utility functions.
universalmotif | universalmotif: Motif class.
universalmotif-class | universalmotif: Motif class.
universalmotif-pkg | universalmotif: Import, Modify and Export Motifs with R
utilities | Utility functions.
utils-motif | Motif-related utility functions.
utils-sequence | Sequence-related utility functions.
view_motifs | Plot motif logos.
write_homer | Export motifs in HOMER format.
write_jaspar | Export motifs in JASPAR format.
write_matrix | Export motifs as raw matrices.
write_meme | Export motifs in MEME format.
write_motifs | Export motifs in universalmotif format.
write_transfac | Export motifs in TRANSFAC format.
[-method | universalmotif: Motif class.
[<--method | universalmotif: Motif class.