Index

A

add_exon_structure() (in module polyase) (in module polyase.structure) add_structure_from_gtf() (in module polyase) (in module polyase.structure)

aggregate_transcripts_to_genes() (in module polyase) (in module polyase.ase_data_loader) AlleleRatioCalculator (class in polyase) (class in polyase.allele_utils)

C

calculate_allelic_ratios() (in module polyase) (in module polyase.allele_utils) calculate_combined_structure_similarity() (in module polyase.structure) calculate_multi_ratios() (in module polyase) (in module polyase.multimapping) calculate_multiple_ratios() (polyase.allele_utils.AlleleRatioCalculator method) (polyase.AlleleRatioCalculator method)

calculate_per_allele_ratios() (in module polyase) (in module polyase.multimapping) calculate_ratios() (polyase.allele_utils.AlleleRatioCalculator method) (polyase.AlleleRatioCalculator method) (polyase.multimapping.MultimappingRatioCalculator method) (polyase.MultimappingRatioCalculator method) calculate_structure_similarity() (in module polyase.structure) convert_pvalue_to_asterisks() (in module polyase.plotting)

F

filter_low_expressed_genes() (in module polyase) (in module polyase.filter)

G

get_ratios_for_synt_id() (polyase.allele_utils.AlleleRatioCalculator method) (polyase.AlleleRatioCalculator method) (polyase.multimapping.MultimappingRatioCalculator method) (polyase.MultimappingRatioCalculator method)

get_top_differential_syntelogs() (in module polyase) (in module polyase.stats)

L

load_ase_data() (in module polyase) (in module polyase.ase_data_loader)

M

module polyase polyase.allele_utils polyase.ase_data_loader polyase.filter polyase.multimapping polyase.plotting polyase.stats polyase.structure

MultimappingRatioCalculator (class in polyase) (class in polyase.multimapping)

P

plot_allele_specific_isoform_structure() (in module polyase) (in module polyase.plotting) plot_allelic_ratios() (in module polyase) (in module polyase.plotting) plot_differential_isoform_usage() (in module polyase) (in module polyase.plotting) plot_top_differential_isoforms() (in module polyase) (in module polyase.plotting) plot_top_differential_syntelogs() (in module polyase) (in module polyase.plotting) plot_top_differential_syntelogs_annotated() (in module polyase) (in module polyase.plotting) polyase module

polyase.allele_utils module polyase.ase_data_loader module polyase.filter module polyase.multimapping module polyase.plotting module polyase.stats module polyase.structure module

S

set_data() (polyase.allele_utils.AlleleRatioCalculator method) (polyase.AlleleRatioCalculator method) (polyase.multimapping.MultimappingRatioCalculator method) (polyase.MultimappingRatioCalculator method)

T

test_allelic_ratios_between_conditions() (in module polyase) (in module polyase.stats) test_allelic_ratios_pairwise() (in module polyase) (in module polyase.stats) test_allelic_ratios_within_conditions() (in module polyase) (in module polyase.stats)

test_differential_isoform_structure() (in module polyase) (in module polyase.stats) test_isoform_DIU_between_conditions() (in module polyase) (in module polyase.stats) test_pairwise_allele_response_between_conditions() (in module polyase) (in module polyase.stats)