Index

A

adjacent_coding_exons() (in module fac.deletion) all_3mers() (in module fac.utils)

all_frames_closed() (in module fac) all_locations (fac.CodingExon property)

B

bar_color() (in module fac.plotting)

bootstrap_series() (in module fac.utils)

C

calibration_accuracy_and_thresholds() (in module fac.models) close_consecutive_coding_exons() (in module fac.deletion)

CodingExon (class in fac) compute_mean_decrease_probability_each() (fac.real_experiments.RealExperimentResultForModel method)

D

DeletionAccuracyDeltaResult (class in fac.deletion)

draw_bases() (in module fac.utils)

E

experiment() (in module fac.deletion) (in module fac.replace_3mer)

experiments() (in module fac.deletion) (in module fac.replace_3mer)

F

fac.deletion.conditions (built-in variable)

filter_models() (fac.real_experiments.FullRealExperimentResult method) FullRealExperimentResult (class in fac.real_experiments)

I

is_stop() (in module fac)

L

length (fac.CodingExon property)

line_color() (in module fac.plotting)

M

map_model_keys() (fac.real_experiments.FullRealExperimentResult method) mean_decrease_probability_each() (fac.real_experiments.FullRealExperimentResult method) mean_effect_masked() (fac.deletion.DeletionAccuracyDeltaResult method)

mean_effect_matrix() (fac.deletion.DeletionAccuracyDeltaResult method) mean_effect_series() (fac.deletion.DeletionAccuracyDeltaResult method) merge() (fac.real_experiments.FullRealExperimentResult class method) ModelToAnalyze (class in fac)

N

no_undesired_changes_mask() (in module fac.replace_3mer)

P

parse_sequence_as_one_hot() (in module fac.utils) plot_adjacent_deletion_results() (in module fac.deletion) plot_by_codon() (in module fac.replace_3mer) plot_by_codon_table() (in module fac.replace_3mer) plot_by_deletion_loc_and_affected_site() (in module fac.deletion) plot_effect_grouped() (in module fac.replace_3mer)

plot_exon_effects_by_orf() (in module fac.deletion) plot_matrix_at_site() (in module fac.deletion) plot_summary() (in module fac.real_experiments) poison_exon_scatterplots() (in module fac.poison_exons) poison_exon_scores() (in module fac.poison_exons) poison_exon_scores_for_model_series() (in module fac.poison_exons) poison_exons_summary_plot() (in module fac.poison_exons)

R

RealExperimentResultForModel (class in fac.real_experiments) Replace3MerResult() (in module fac.replace_3mer)

run_on_all_adjacent_deletions() (in module fac.deletion) run_on_all_adjacent_deletions_for_multiple_series() (in module fac.deletion)

S

sequence_to_codons() (in module fac)

T

text (fac.CodingExon property)

to_dict() (fac.CodingExon method)