Index

A

align_pms() (in module smeagol.matrices)

C

check_pfm() (in module smeagol.matrices) check_ppm() (in module smeagol.matrices) check_pwm() (in module smeagol.matrices) choose_cluster_representative_pms() (in module smeagol.matrices)

choose_representative_pm() (in module smeagol.matrices) cluster_pms() (in module smeagol.matrices) collect_data() (in module smeagol.aggregate) cos_sim() (in module smeagol.matrices) count_in_sliding_windows() (in module smeagol.scan)

E

enrich_in_genome() (in module smeagol.enrich) enrich_in_sliding_windows() (in module smeagol.enrich)

enrich_in_window() (in module smeagol.enrich) entropy() (in module smeagol.matrices) examine_thresholds() (in module smeagol.enrich)

G

get_Seq() (in module smeagol.utils)

get_site_seq() (in module smeagol.utils) get_tiling_windows_over_genome() (in module smeagol.utils)

I

ids (smeagol.encode.SeqEncoding attribute)

integer_encode() (in module smeagol.encode)

L

len (smeagol.encode.SeqEncoding attribute) load_attract() (in module smeagol.io)

load_rbpdb() (in module smeagol.io) load_smeagol_PWMset() (in module smeagol.io)

M

matrix_correlation() (in module smeagol.matrices) module smeagol smeagol.aggregate smeagol.encode smeagol.enrich smeagol.io smeagol.matrices smeagol.scan smeagol.utils smeagol.variant smeagol.visualize

N

names (smeagol.encode.SeqEncoding attribute)

ncorr() (in module smeagol.matrices) normalize_pm() (in module smeagol.matrices)

O

one_hot_encode() (in module smeagol.encode)

order_pms() (in module smeagol.matrices)

P

pairwise_ncorrs() (in module smeagol.matrices) pfm_to_ppm() (in module smeagol.matrices) plot_background() (in module smeagol.visualize) plot_binned_count_dist() (in module smeagol.visualize) plot_clustermap() (in module smeagol.visualize) plot_clustermap_annot() (in module smeagol.visualize)

plot_ppm() (in module smeagol.visualize) plot_pwm() (in module smeagol.visualize) position_wise_ic() (in module smeagol.matrices) ppm_logo() (in module smeagol.visualize) ppm_to_pwm() (in module smeagol.matrices) pwm_logo() (in module smeagol.visualize) pwm_to_ppm() (in module smeagol.matrices)

R

read_bg_seqs() (in module smeagol.utils) read_fasta() (in module smeagol.io)

read_pms_from_dir() (in module smeagol.io) read_pms_from_file() (in module smeagol.io)

S

scan_sequences() (in module smeagol.scan) score_site() (in module smeagol.scan) senses (smeagol.encode.SeqEncoding attribute) SeqEncoding (class in smeagol.encode) SeqGroups (class in smeagol.encode) seqs (smeagol.encode.SeqEncoding attribute) shuffle_records() (in module smeagol.utils) sliding_window_count_plot() (in module smeagol.visualize) sliding_window_enrichment_plot() (in module smeagol.visualize) smeagol module smeagol.aggregate module smeagol.encode module

smeagol.enrich module smeagol.io module smeagol.matrices module smeagol.scan module smeagol.utils module smeagol.variant module smeagol.visualize module

T

trim_ppm() (in module smeagol.matrices)

V

variant_effect_on_sites() (in module smeagol.variant)

W

write_fasta() (in module smeagol.io)