Index

_

__init__() (rna_majiq.Contigs method), [1] (rna_majiq.DeltaPsi method), [1] (rna_majiq.DeltaPsiPMF method), [1] (rna_majiq.DPsiPrior method), [1] (rna_majiq.Events method), [1] (rna_majiq.ExonConnections method), [1] (rna_majiq.Exons method), [1] (rna_majiq.ExperimentThresholds method), [1] (rna_majiq.GeneIntrons method), [1] (rna_majiq.GeneJunctions method), [1] (rna_majiq.GeneJunctionsAccumulator method), [1] (rna_majiq.Genes method), [1] (rna_majiq.GroupIntronsGenerator method), [1] (rna_majiq.GroupJunctionsGenerator method), [1] (rna_majiq.Heterogen method), [1] (rna_majiq.PassedJunctionsGenerator method), [1] (rna_majiq.PsiControlsSummary method), [1] (rna_majiq.PsiCoverage method), [1] (rna_majiq.PsiOutliers method), [1] (rna_majiq.SimplifierGroup method), [1] (rna_majiq.SJExperiment method), [1] (rna_majiq.SJIntronsBins method), [1] (rna_majiq.SJJunctionsBins method), [1] (rna_majiq.SpliceGraph method), [1] (rna_majiq.UniqueEventsMasks method), [1]

_simplify_all() (rna_majiq.GeneIntrons method), [1] (rna_majiq.GeneJunctions method), [1] _unsimplify_all() (rna_majiq.GeneIntrons method), [1] (rna_majiq.GeneJunctions method), [1]

A

accumulated() (rna_majiq.GeneJunctionsAccumulator method), [1] add() (rna_majiq.GeneJunctionsAccumulator method), [1] add_experiment() (rna_majiq.GroupIntronsGenerator method), [1] (rna_majiq.GroupJunctionsGenerator method), [1] (rna_majiq.SimplifierGroup method), [1]

add_group() (rna_majiq.PassedJunctionsGenerator method), [1] approximate_alpha (rna_majiq.PsiCoverage property), [1] approximate_beta (rna_majiq.PsiCoverage property), [1] approximate_discretized_pmf() (rna_majiq.PsiCoverage method), [1] approximate_quantile() (rna_majiq.PsiCoverage method), [1] approximate_stats() (rna_majiq.Heterogen method), [1]

B

bootstrap_alpha (rna_majiq.PsiCoverage property), [1] bootstrap_beta (rna_majiq.PsiCoverage property), [1] bootstrap_coverage (rna_majiq.PsiCoverage property), [1] bootstrap_posterior (rna_majiq.DeltaPsi property), [1] bootstrap_psi_mean (rna_majiq.PsiCoverage property), [1] bootstrap_psi_mean_legacy (rna_majiq.PsiCoverage property), [1]

bootstrap_psi_mean_population_median (rna_majiq.PsiCoverage property), [1] bootstrap_psi_mean_population_quantile() (rna_majiq.PsiCoverage method), [1] bootstrap_psi_std (rna_majiq.PsiCoverage property), [1] bootstrap_total (rna_majiq.PsiCoverage property), [1] build_group() (rna_majiq.GeneIntrons method), [1] (rna_majiq.GeneJunctions method), [1] builder() (rna_majiq.GeneJunctions method), [1]

C

connection_denovo() (rna_majiq.Events method), [1] connection_end() (rna_majiq.Events method), [1] connection_gene_idx() (rna_majiq.Events method), [1] connection_idx (rna_majiq.Events property), [1] connection_other_exon_idx() (rna_majiq.Events method), [1]

connection_ref_exon_idx (rna_majiq.Events property), [1] connection_start() (rna_majiq.Events method), [1] connections_slice_for_event() (rna_majiq.Events method), [1] constitutive() (rna_majiq.ExonConnections method), [1] Contigs (class in rna_majiq), [1] create_connecting() (rna_majiq.ExonConnections class method), [1]

D

dataset() (rna_majiq.DeltaPsi method), [1] (rna_majiq.Heterogen method), [1] DeltaPsi (class in rna_majiq), [1]

DeltaPsiPMF (class in rna_majiq), [1] df (rna_majiq.Events property), [1] DPsiPrior (class in rna_majiq), [1]

E

e_idx (rna_majiq.Events property), [1] ec_dataframe() (rna_majiq.Events method), [1] ec_idx (rna_majiq.Events property), [1] ec_idx_end (rna_majiq.Events property), [1] ec_idx_start (rna_majiq.Events property), [1] empirical_update() (rna_majiq.DPsiPrior method), [1] empty_introns() (rna_majiq.Exons method), [1]

event_passed (rna_majiq.PsiCoverage property), [1] event_type (rna_majiq.Events property), [1] Events (class in rna_majiq), [1] ExonConnections (class in rna_majiq), [1] Exons (class in rna_majiq), [1] exons (rna_majiq.Events property), [1] ExperimentThresholds (class in rna_majiq), [1]

F

filter_passed() (rna_majiq.GeneIntrons method), [1] from_bam() (rna_majiq.SJExperiment class method), [1] from_components() (rna_majiq.SpliceGraph class method), [1] from_gff3() (rna_majiq.SpliceGraph class method), [1] from_sj_lsvs() (rna_majiq.PsiCoverage class method), [1]

from_zarr() (rna_majiq.Events class method), [1] (rna_majiq.PsiControlsSummary class method), [1] (rna_majiq.PsiCoverage class method), [1] (rna_majiq.SJExperiment class method), [1] (rna_majiq.SpliceGraph class method), [1]

G

GeneIntrons (class in rna_majiq), [1] GeneJunctions (class in rna_majiq), [1] GeneJunctionsAccumulator (class in rna_majiq), [1] Genes (class in rna_majiq), [1]

get_events() (rna_majiq.PsiControlsSummary method), [1] (rna_majiq.PsiCoverage method), [1] get_passed() (rna_majiq.PassedJunctionsGenerator method), [1] GroupIntronsGenerator (class in rna_majiq), [1] GroupJunctionsGenerator (class in rna_majiq), [1]

H

Heterogen (class in rna_majiq), [1]

I

infer_with_junctions() (rna_majiq.Exons method), [1] introns (rna_majiq.Events property), [1] (rna_majiq.SJExperiment property), [1]

is_intron (rna_majiq.Events property), [1]

J

junctions (rna_majiq.Events property), [1] (rna_majiq.SJExperiment property), [1]

L

lsvs() (rna_majiq.ExonConnections method), [1]

M

mask_events() (rna_majiq.PsiCoverage method), [1]

mean (rna_majiq.DeltaPsiPMF property), [1]

N

num_bootstraps (rna_majiq.PsiCoverage property), [1] num_connections (rna_majiq.PsiCoverage property), [1]

num_passed (rna_majiq.PsiControlsSummary property), [1] (rna_majiq.PsiCoverage property), [1] num_prefixes (rna_majiq.PsiCoverage property), [1]

P

passed_min_experiments() (rna_majiq.PsiControlsSummary method), [1] (rna_majiq.PsiCoverage method), [1] PassedJunctionsGenerator (class in rna_majiq), [1] potential_introns() (rna_majiq.Exons method), [1] prefixes (rna_majiq.PsiControlsSummary property), [1] (rna_majiq.PsiCoverage property), [1] probability_changing() (rna_majiq.DeltaPsiPMF method), [1]

probability_nonchanging() (rna_majiq.DeltaPsiPMF method), [1] psi_median (rna_majiq.PsiControlsSummary property), [1] psi_quantile (rna_majiq.PsiControlsSummary property), [1] psi_range (rna_majiq.PsiControlsSummary property), [1] PsiControlsSummary (class in rna_majiq), [1] PsiCoverage (class in rna_majiq), [1] PsiOutliers (class in rna_majiq), [1]

Q

q (rna_majiq.PsiControlsSummary property), [1]

R

raw_alpha (rna_majiq.PsiCoverage property), [1] raw_beta (rna_majiq.PsiCoverage property), [1] raw_coverage (rna_majiq.PsiCoverage property), [1] raw_psi_mean (rna_majiq.PsiCoverage property), [1] raw_psi_mean_population_median (rna_majiq.PsiCoverage property), [1] raw_psi_mean_population_quantile() (rna_majiq.PsiCoverage method), [1]

raw_psi_std (rna_majiq.PsiCoverage property), [1] raw_stats() (rna_majiq.Heterogen method), [1] raw_total (rna_majiq.PsiCoverage property), [1] ref_exon_idx (rna_majiq.Events property), [1] rng_resize() (in module rna_majiq), [1] rng_seed() (in module rna_majiq), [1]

S

simplifier() (rna_majiq.ExonConnections method), [1] SimplifierGroup (class in rna_majiq), [1] SJExperiment (class in rna_majiq), [1] SJIntronsBins (class in rna_majiq), [1]

SJJunctionsBins (class in rna_majiq), [1] SpliceGraph (class in rna_majiq), [1] standard_deviation (rna_majiq.DeltaPsiPMF property), [1] sum() (rna_majiq.PsiCoverage method), [1]

T

to_zarr() (rna_majiq.Events method), [1] (rna_majiq.PsiControlsSummary method), [1] (rna_majiq.PsiCoverage method), [1] (rna_majiq.SJExperiment method), [1] (rna_majiq.SpliceGraph method), [1]

to_zarr_slice() (rna_majiq.PsiCoverage method), [1] to_zarr_slice_init() (rna_majiq.PsiCoverage class method), [1]

U

unique_events_mask() (rna_majiq.Events method), [1] UniqueEventsMasks (class in rna_majiq), [1] update_connections() (rna_majiq.SimplifierGroup method), [1]

update_flags_from() (rna_majiq.GeneIntrons method), [1] update_introns() (rna_majiq.GroupIntronsGenerator method), [1] updated() (rna_majiq.PsiCoverage method), [1]

W

with_updated_exon_connections() (rna_majiq.SpliceGraph method), [1]