GimmeMotifs
0.18.0
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Simple examples
Tutorials
Command-line reference
API documentation
Examples
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Index
A
|
B
|
C
|
G
|
H
|
I
|
L
|
M
|
P
|
R
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S
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T
|
W
A
akl() (in module gimmemotifs.comparison)
average_motifs() (gimmemotifs.motif.Motif method)
B
best_match() (gimmemotifs.scanner.Scanner method)
best_score() (gimmemotifs.scanner.Scanner method)
C
calc_stats() (in module gimmemotifs.stats)
calc_stats_iterator() (in module gimmemotifs.stats)
chisq() (in module gimmemotifs.comparison)
compare_motifs() (gimmemotifs.comparison.MotifComparer method)
consensus (gimmemotifs.motif.Motif property)
consensus_scan() (gimmemotifs.motif.Motif method)
count() (gimmemotifs.scanner.Scanner method)
create() (gimmemotifs.maelstrom.Moap class method)
G
get_all_scores() (gimmemotifs.comparison.MotifComparer method)
get_best_matches() (gimmemotifs.comparison.MotifComparer method)
get_closest_match() (gimmemotifs.comparison.MotifComparer method)
gimme_motifs() (in module gimmemotifs.motif)
gimmemotifs.comparison
module
gimmemotifs.denovo
module
gimmemotifs.maelstrom
module
gimmemotifs.motif
module
gimmemotifs.scanner
module
gimmemotifs.stats
module
H
hash (gimmemotifs.motif.Motif property)
I
ic_pos() (gimmemotifs.motif.Motif method)
information_content (gimmemotifs.motif.Motif property)
L
list_classification_predictors() (gimmemotifs.maelstrom.Moap class method)
list_predictors() (gimmemotifs.maelstrom.Moap class method)
list_regression_predictors() (gimmemotifs.maelstrom.Moap class method)
M
MaelstromResult (class in gimmemotifs.maelstrom)
max_score (gimmemotifs.motif.Motif property)
min_score (gimmemotifs.motif.Motif property)
Moap (class in gimmemotifs.maelstrom)
moap() (in module gimmemotifs.maelstrom)
module
gimmemotifs.comparison
gimmemotifs.denovo
gimmemotifs.maelstrom
gimmemotifs.motif
gimmemotifs.scanner
gimmemotifs.stats
Motif (class in gimmemotifs.motif)
motif_from_align() (in module gimmemotifs.motif)
motif_from_consensus() (in module gimmemotifs.motif)
MotifComparer (class in gimmemotifs.comparison)
P
parse_motifs() (in module gimmemotifs.motif)
pfm_to_ppm() (gimmemotifs.motif.Motif method)
plot_ensembl_logo() (gimmemotifs.motif.Motif method)
plot_heatmap() (gimmemotifs.maelstrom.MaelstromResult method)
plot_logo() (gimmemotifs.motif.Motif method)
plot_scores() (gimmemotifs.maelstrom.MaelstromResult method)
progress (gimmemotifs.scanner.Scanner property)
pwm_max_score() (gimmemotifs.motif.Motif method)
pwm_min_score() (gimmemotifs.motif.Motif method)
pwm_scan_score() (gimmemotifs.motif.Motif method)
pwm_scan_to_gff() (gimmemotifs.motif.Motif method)
R
randomize() (gimmemotifs.motif.Motif method)
rank_motifs() (in module gimmemotifs.stats)
rc() (gimmemotifs.motif.Motif method)
read_motifs() (in module gimmemotifs.motif)
register_predictor() (gimmemotifs.maelstrom.Moap class method)
run_maelstrom() (in module gimmemotifs.maelstrom)
S
sample() (gimmemotifs.motif.Motif method)
scan() (gimmemotifs.motif.Motif method)
(gimmemotifs.scanner.Scanner method)
scan_all() (gimmemotifs.motif.Motif method)
scan_regionfile_to_table() (in module gimmemotifs.scanner)
scan_to_best_match() (in module gimmemotifs.scanner)
scan_to_file() (in module gimmemotifs.scanner)
Scanner (class in gimmemotifs.scanner)
score_kmer() (gimmemotifs.motif.Motif method)
seqcor() (in module gimmemotifs.comparison)
set_background() (gimmemotifs.scanner.Scanner method)
set_genome() (gimmemotifs.scanner.Scanner method)
set_threshold() (gimmemotifs.scanner.Scanner method)
shuffle() (gimmemotifs.motif.Motif method)
ssd() (in module gimmemotifs.comparison)
T
to_consensus() (gimmemotifs.motif.Motif method)
to_meme() (gimmemotifs.motif.Motif method)
to_motevo() (gimmemotifs.motif.Motif method)
to_ppm() (gimmemotifs.motif.Motif method)
to_pwm() (gimmemotifs.motif.Motif method)
to_transfac() (gimmemotifs.motif.Motif method)
total_count() (gimmemotifs.scanner.Scanner method)
trim() (gimmemotifs.motif.Motif method)
W
write_stats() (in module gimmemotifs.stats)