universalmotif
Import, Modify, and Export Motifs with R

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81
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universalmotif: Import, Modify, and Export Motifs with R
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API

API for universalmotif
Import, Modify, and Export Motifs with R

Global functions
.internal_convert Source code
.onUnload Source code
ArabidopsisMotif Man page
ArabidopsisPromoters Man page
JASPAR2018_CORE_DBSCORES Man page
MATRIX_ppm_to_pwm Source code
[,universalmotif-method Man page
[<-,universalmotif-method Man page
add_gap Man page Source code
add_gap_dots_cpp Source code
add_multi_cpp Source code
add_multifreq Man page Source code
adjust_rc_hits Source code
all_checks_collapse Source code
ape_fun Source code
as.data.frame Man page
as.data.frame,universalmotif-method Man page
branch_and_bound_cpp_exposed Source code
c.universalmotif Source code
calc_scores Source code
calc_seq_probs_cpp Source code
calc_wins Source code
cbind Man page
cbind,universalmotif-method Man page
check_db_scores Source code
check_extrainfo Source code
check_fun_params Source code
check_k_lets Source code
check_list Source code
check_meme_alph_type Source code
check_meme_version Source code
check_mot_sizes Source code
check_right_side Source code
colMeans Man page
colMeans,universalmotif-method Man page
colSums Man page
colSums,universalmotif-method Man page
collapse2 Source code
collapse_cols_mat Source code
collapse_cpp Source code
collapse_rows_df Source code
collapse_rows_mat Source code
colnames Man page
colnames,universalmotif-method Man page
comb2_cpp Source code
compare_columns Man page Source code
compare_columns_cpp Source code
compare_motifs Man page Source code
compare_motifs_all Source code
compare_motifs_all_cpp Source code
compare_motifs_cpp Source code
compare_motifs_reporter Source code
consensus_to_ppm Man page Source code
consensus_to_ppmAA Man page Source code
consensus_to_ppmAAC Source code
consensus_to_ppmC Source code
convert_from_icm Source code
convert_from_pcm Source code
convert_from_ppm Source code
convert_from_pwm Source code
convert_mat_type_from_ppm Source code
convert_motifs Man page
convert_motifs,ICMatrix-method Man page
convert_motifs,Motif-method Man page
convert_motifs,MotifList-method Man page
convert_motifs,PFMatrix-method Man page
convert_motifs,PWM-method Man page
convert_motifs,PWMatrix-method Man page
convert_motifs,TFFMFirst-method Man page
convert_motifs,XMatrixList-method Man page
convert_motifs,list-method Man page
convert_motifs,matrix-method Man page
convert_motifs,pcm-method Man page
convert_motifs,pfm-method Man page
convert_motifs,pwm-method Man page
convert_motifs,universalmotif-method Man page
convert_to_biostrings_pwm Source code
convert_to_motifstack_pcm Source code
convert_to_motifstack_pfm Source code
convert_to_motiv_pwm2 Source code
convert_to_pwmenrich_pwm Source code
convert_to_rgadem_motif Source code
convert_to_seqlogo_pwm Source code
convert_to_tfbstools_matrix Source code
convert_to_tfbstools_tffmfirst Source code
convert_type Man page Source code
convert_type_internal Source code
convert_type_single Source code
count_klets Man page Source code
count_klets_alph_cpp Source code
count_klets_cpp Source code
create_motif Man page
create_motif,AAStringSet-method Man page
create_motif,BStringSet-method Man page
create_motif,DNAStringSet-method Man page
create_motif,RNAStringSet-method Man page
create_motif,character-method Man page
create_motif,matrix-method Man page
create_motif,missing-method Man page
create_motif,numeric-method Man page
create_sequences Man page Source code
create_sequences_cpp Source code
enrich_motifs Man page Source code
enrich_mots2 Source code
enrich_mots2_subworker Source code
examplemotif Man page
examplemotif2 Man page
expand_scores Source code
filter_motifs Man page Source code
find_best_dist Source code
fix_mots Source code
format_pos Source code
generate_motif Source code
get_bkg Man page Source code
get_bkgs Source code
get_comp_indices Source code
get_comparison_matrix Source code
get_comparisons Source code
get_consensus Man page Source code
get_consensusAA Man page Source code
get_consensusAAC Source code
get_consensusC Source code
get_custom_meme_alph Source code
get_default_meme_alph Source code
get_gaplocs Source code
get_klets Man page Source code
get_klets_cpp Source code
get_matches Man page Source code
get_meme_alph Source code
get_meme_alph_len Source code
get_nsites Source code
get_params Source code
get_rid_of_dupes Source code
get_scores Man page Source code
get_submotifs Source code
ggtree_fun Source code
icm_to_ppm Man page Source code
icm_to_ppmC Source code
initialize,universalmotif-method Man page
kern_fun Source code
lapply_ Source code
letter_freqs Source code
linbin_cpp Source code
log_string_pval Man page Source code
make_DBscores Man page Source code
make_DBscores_motifs Source code
make_DBscores_v1 Source code
make_DBscores_v3 Source code
make_blank_motif Source code
make_umot Source code
mapply_ Source code
mask_seqs Man page Source code
meme_cb Source code
merge_motifs Man page Source code
merge_motifs_all Source code
merge_motifs_cpp Source code
min_max_doubles Source code
min_max_ints Source code
motif_clusters Source code
motif_finder Source code
motif_peaks Man page Source code
motif_pvalue Man page Source code
motif_pvalue_bkg Source code
motif_pvalue_cpp Source code
motif_rc Man page Source code
motif_rc_internal Source code
motif_score Man page Source code
motif_score_cpp Source code
motif_score_min Source code
motif_tree Man page Source code
motifs_to_list Source code
motifs_to_umot Source code
ncol Man page
ncol,universalmotif-method Man page
new_bkg Source code
normalize Man page
normalize,universalmotif-method Man page
nrow Man page
nrow,universalmotif-method Man page
parse_args Source code
parse_matrix Source code
parse_meta Source code
parse_motifs Source code
parse_multi Source code
paths_alph_unsort Source code
paths_to_alph Source code
pcm_to_ppm Man page Source code
pcm_to_ppmC Source code
pdate Source code
peakfinder_cpp Source code
position_icscore Man page Source code
position_icscoreC Source code
ppm_to_icm Man page Source code
ppm_to_icmC Source code
ppm_to_pcm Man page Source code
ppm_to_pcmC Source code
ppm_to_pwm Man page Source code
ppm_to_pwmC Source code
print_pb Source code
prob_match Man page Source code
prob_match_bkg Man page Source code
process_gapped_motifs Source code
processx_fun Source code
pval_extractor Source code
pval_str2double Source code
pwm_to_ppm Man page Source code
pwm_to_ppmC Source code
read_cisbp Man page Source code
read_homer Man page Source code
read_jaspar Man page Source code
read_matrix Man page Source code
read_meme Man page Source code
read_motifs Man page Source code
read_motifs_1_0 Source code
read_motifs_1_2 Source code
read_motifs_single Source code
read_motifs_single_pre Source code
read_transfac Man page Source code
read_uniprobe Man page Source code
reexports Man page
round_motif Man page Source code
round_motif_cpp Source code
rowMeans Man page
rowMeans,universalmotif-method Man page
rowSums Man page
rowSums,universalmotif-method Man page
rownames Man page
rownames,universalmotif-method Man page
run_meme Man page Source code
sample_k1 Source code
sample_motif Source code
sample_motif_ Source code
sample_single Source code
sample_sites Man page Source code
scan_sequences Man page Source code
scan_sequences_cpp Source code
score_match Man page Source code
show,universalmotif-method Man page
shuffle_euler_cpp Source code
shuffle_k1 Source code
shuffle_k1_cpp Source code
shuffle_linear Source code
shuffle_linear_cpp Source code
shuffle_markov_cpp Source code
shuffle_motifs Man page Source code
shuffle_new_mot Source code
shuffle_sequences Man page Source code
shuffle_string Man page Source code
sort_unique_cpp Source code
split_by_motif_enrich Source code
split_gapped Source code
split_seq_by_win Source code
subset Man page
subset,universalmotif-method Man page
summarise_motifs Man page Source code
summarise_motifs_cpp Source code
switch_alph Man page Source code
table_cpp Source code
to_meme_bkg Source code
to_meme_bkg_single Source code
trim_motif_internal Source code
trim_motifs Man page Source code
ungap Man page Source code
ungap_single Source code
universalmotif Man page
universalmotif-class Man page
universalmotif-pkg Man page
universalmotif_cpp Source code
universalmotif_to_list Source code
update_pb Source code
utilities Man page
utils-motif Man page
utils-sequence Man page
validObject_universalmotif Source code
view_motifs Man page Source code
view_motifs_prep Source code
wmsg2 Source code
write_homer Man page Source code
write_jaspar Man page Source code
write_matrix Man page Source code
write_meme Man page Source code
write_motifs Man page Source code
write_motifs2_single Source code
write_transfac Man page Source code
universalmotif documentation built on April 8, 2021, 6 p.m.

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