genophenocorr
0.1
Installation & Tutorial
Installation
Tutorial
User guide
API reference
genophenocorr
Index
Index
A
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
A
all_patients (genophenocorr.model.Cohort property)
all_phenotypes (genophenocorr.model.Cohort property)
all_proteins (genophenocorr.model.Cohort property)
all_transcripts (genophenocorr.model.Cohort property)
all_variants (genophenocorr.model.Cohort property)
alt (genophenocorr.model.VariantCoordinates attribute)
(genophenocorr.model.VariantCoordinates property)
analysis_cohort (genophenocorr.analysis.CohortAnalysis attribute)
(genophenocorr.analysis.CohortAnalysis property)
analysis_patients (genophenocorr.analysis.CohortAnalysis attribute)
(genophenocorr.analysis.CohortAnalysis property)
analysis_transcript (genophenocorr.analysis.CohortAnalysis attribute)
(genophenocorr.analysis.CohortAnalysis property)
anchor() (genophenocorr.view.CohortViewer static method)
annotate() (genophenocorr.preprocessing.FunctionalAnnotator method)
(genophenocorr.preprocessing.ProtCachingFunctionalAnnotator method)
(genophenocorr.preprocessing.ProteinMetadataService method)
(genophenocorr.preprocessing.UniprotProteinMetadataService method)
(genophenocorr.preprocessing.VarCachingFunctionalAnnotator method)
(genophenocorr.preprocessing.VepFunctionalAnnotator method)
as_string() (genophenocorr.model.VariantCoordinates method)
,
[1]
C
cat_id (genophenocorr.analysis.predicate.PatientCategory property)
categories (genophenocorr.analysis.predicate.PolyPredicate property)
categories() (genophenocorr.analysis.predicate.ExonPredicate method)
(genophenocorr.analysis.predicate.HPOPresentPredicate method)
(genophenocorr.analysis.predicate.ProtFeaturePredicate method)
(genophenocorr.analysis.predicate.ProtFeatureTypePredicate method)
(genophenocorr.analysis.predicate.VariantEffectPredicate method)
(genophenocorr.analysis.predicate.VariantPredicate method)
change_length (genophenocorr.model.VariantCoordinates attribute)
(genophenocorr.model.VariantCoordinates property)
chrom (genophenocorr.model.VariantCoordinates attribute)
(genophenocorr.model.VariantCoordinates property)
CODING_SEQUENCE_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
Cohort (class in genophenocorr.model)
CohortAnalysis (class in genophenocorr.analysis)
CohortViewer (class in genophenocorr.view)
compare_by_exon() (genophenocorr.analysis.CohortAnalysis method)
compare_by_protein_feature() (genophenocorr.analysis.CohortAnalysis method)
compare_by_protein_feature_type() (genophenocorr.analysis.CohortAnalysis method)
compare_by_variant() (genophenocorr.analysis.CohortAnalysis method)
compare_by_variant_type() (genophenocorr.analysis.CohortAnalysis method)
configure_caching_patient_creator() (in module genophenocorr.preprocessing)
create() (genophenocorr.model.ProteinFeature static method)
create_patient() (genophenocorr.preprocessing.PatientCreator method)
(genophenocorr.preprocessing.PhenopacketPatientCreator method)
create_phenotype() (genophenocorr.preprocessing.PhenotypeCreator method)
create_variant_from_scratch() (genophenocorr.model.Variant static method)
D
description (genophenocorr.analysis.predicate.PatientCategory property)
DOMAIN (genophenocorr.model.FeatureType attribute)
,
[1]
domains() (genophenocorr.model.ProteinMetadata method)
,
[1]
DOWNSTREAM_GENE_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
E
end (genophenocorr.model.FeatureInfo attribute)
(genophenocorr.model.FeatureInfo property)
(genophenocorr.model.VariantCoordinates attribute)
(genophenocorr.model.VariantCoordinates property)
ExonPredicate (class in genophenocorr.analysis.predicate)
F
FEATURE_ELONGATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
FEATURE_TRUNCATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
feature_type (genophenocorr.model.ProteinFeature property)
FeatureInfo (class in genophenocorr.model)
FeatureType (class in genophenocorr.model)
find_coordinates() (genophenocorr.preprocessing.PhenopacketVariantCoordinateFinder method)
(genophenocorr.preprocessing.VariantCoordinateFinder method)
FIVE_PRIME_UTR_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
FRAMESHIFT_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
from_patients() (genophenocorr.model.Cohort static method)
from_term() (genophenocorr.model.Phenotype static method)
FunctionalAnnotator (class in genophenocorr.preprocessing)
G
gene_id (genophenocorr.model.TranscriptAnnotation attribute)
(genophenocorr.model.TranscriptAnnotation property)
genophenocorr
module
genophenocorr.analysis
module
genophenocorr.analysis.predicate
module
genophenocorr.constants
module
genophenocorr.constants.variant_effects
module
genophenocorr.data
module
genophenocorr.model
module
genophenocorr.preprocessing
module
genophenocorr.view
module
genotype (genophenocorr.model.Variant attribute)
(genophenocorr.model.Variant property)
(genophenocorr.model.VariantCoordinates attribute)
(genophenocorr.model.VariantCoordinates property)
get_annotations() (genophenocorr.preprocessing.ProteinAnnotationCache method)
(genophenocorr.preprocessing.VariantAnnotationCache method)
get_toy_cohort() (in module genophenocorr.data)
H
hgvsc_id (genophenocorr.model.TranscriptAnnotation attribute)
(genophenocorr.model.TranscriptAnnotation property)
hpo_anchor() (genophenocorr.view.CohortViewer static method)
hpo_term_counts_table() (genophenocorr.view.CohortViewer method)
HPOPresentPredicate (class in genophenocorr.analysis.predicate)
html_row() (genophenocorr.view.CohortViewer static method)
I
identifier (genophenocorr.model.Phenotype attribute)
(genophenocorr.model.Phenotype property)
include_large_SV (genophenocorr.analysis.CohortAnalysis attribute)
(genophenocorr.analysis.CohortAnalysis property)
include_unmeasured (genophenocorr.analysis.CohortAnalysis attribute)
(genophenocorr.analysis.CohortAnalysis property)
INCOMPLETE_TERMINAL_CODON_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
info (genophenocorr.model.ProteinFeature property)
INFRAME_DELETION (genophenocorr.constants.variant_effects.VariantEffect attribute)
INFRAME_INSERTION (genophenocorr.constants.variant_effects.VariantEffect attribute)
INTERGENIC_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
INTRON_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
is_recessive (genophenocorr.analysis.CohortAnalysis attribute)
(genophenocorr.analysis.CohortAnalysis property)
is_structural() (genophenocorr.model.VariantCoordinates method)
,
[1]
issues (genophenocorr.preprocessing.PhenotypeValidationException property)
L
label (genophenocorr.model.ProteinMetadata attribute)
(genophenocorr.model.ProteinMetadata property)
list_all_patients() (genophenocorr.model.Cohort method)
list_all_phenotypes() (genophenocorr.model.Cohort method)
list_all_proteins() (genophenocorr.model.Cohort method)
list_all_variants() (genophenocorr.model.Cohort method)
list_data_by_tx() (genophenocorr.model.Cohort method)
load_phenopacket_folder() (in module genophenocorr.preprocessing)
M
MATURE_MIRNA_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
min_perc_patients_w_hpo (genophenocorr.analysis.CohortAnalysis attribute)
(genophenocorr.analysis.CohortAnalysis property)
MISSENSE_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
module
genophenocorr
genophenocorr.analysis
genophenocorr.analysis.predicate
genophenocorr.constants
genophenocorr.constants.variant_effects
genophenocorr.data
genophenocorr.model
genophenocorr.preprocessing
genophenocorr.view
MOTIF (genophenocorr.model.FeatureType attribute)
,
[1]
motifs() (genophenocorr.model.ProteinMetadata method)
,
[1]
N
name (genophenocorr.analysis.predicate.PatientCategory property)
(genophenocorr.model.FeatureInfo attribute)
(genophenocorr.model.FeatureInfo property)
(genophenocorr.model.Phenotype attribute)
(genophenocorr.model.Phenotype property)
NMD_TRANSCRIPT_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
NON_CODING_TRANSCRIPT_EXON_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
NON_CODING_TRANSCRIPT_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
NOT_MEASURED (genophenocorr.analysis.predicate.HPOPresentPredicate attribute)
NOT_OBSERVED (genophenocorr.analysis.predicate.HPOPresentPredicate attribute)
O
OBSERVED (genophenocorr.analysis.predicate.HPOPresentPredicate attribute)
observed (genophenocorr.model.Phenotype attribute)
(genophenocorr.model.Phenotype property)
overlapping_exons (genophenocorr.model.TranscriptAnnotation attribute)
(genophenocorr.model.TranscriptAnnotation property)
P
Patient (class in genophenocorr.model)
patient_id (genophenocorr.model.Patient attribute)
(genophenocorr.model.Patient property)
PatientCategory (class in genophenocorr.analysis.predicate)
PatientCreator (class in genophenocorr.preprocessing)
PhenopacketPatientCreator (class in genophenocorr.preprocessing)
PhenopacketVariantCoordinateFinder (class in genophenocorr.preprocessing)
Phenotype (class in genophenocorr.model)
PhenotypeCreator (class in genophenocorr.preprocessing)
phenotypes (genophenocorr.model.Patient attribute)
(genophenocorr.model.Patient property)
PhenotypeValidationException
PolyPredicate (class in genophenocorr.analysis.predicate)
ProtCachingFunctionalAnnotator (class in genophenocorr.preprocessing)
protein_affected (genophenocorr.model.TranscriptAnnotation attribute)
(genophenocorr.model.TranscriptAnnotation property)
PROTEIN_ALTERING_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
protein_effect_location (genophenocorr.model.TranscriptAnnotation attribute)
(genophenocorr.model.TranscriptAnnotation property)
protein_features (genophenocorr.model.ProteinMetadata attribute)
(genophenocorr.model.ProteinMetadata property)
protein_id (genophenocorr.model.ProteinMetadata attribute)
(genophenocorr.model.ProteinMetadata property)
ProteinAnnotationCache (class in genophenocorr.preprocessing)
ProteinFeature (class in genophenocorr.model)
ProteinMetadata (class in genophenocorr.model)
ProteinMetadataService (class in genophenocorr.preprocessing)
proteins (genophenocorr.model.Patient attribute)
(genophenocorr.model.Patient property)
ProtFeaturePredicate (class in genophenocorr.analysis.predicate)
ProtFeatureTypePredicate (class in genophenocorr.analysis.predicate)
R
ref (genophenocorr.model.VariantCoordinates attribute)
(genophenocorr.model.VariantCoordinates property)
REGION (genophenocorr.model.FeatureType attribute)
,
[1]
regions() (genophenocorr.model.ProteinMetadata method)
,
[1]
REGULATORY_REGION_ABLATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
REGULATORY_REGION_AMPLIFICATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
REGULATORY_REGION_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
REPEAT (genophenocorr.model.FeatureType attribute)
,
[1]
repeats() (genophenocorr.model.ProteinMetadata method)
,
[1]
S
SEQUENCE_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
SimplePredicate (class in genophenocorr.analysis.predicate)
SPLICE_ACCEPTOR_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
SPLICE_DONOR_5TH_BASE_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
SPLICE_DONOR_REGION_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
SPLICE_DONOR_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
SPLICE_POLYPYRIMIDINE_TRACT_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
SPLICE_REGION_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
start (genophenocorr.model.FeatureInfo attribute)
(genophenocorr.model.FeatureInfo property)
(genophenocorr.model.VariantCoordinates attribute)
(genophenocorr.model.VariantCoordinates property)
START_LOST (genophenocorr.constants.variant_effects.VariantEffect attribute)
START_RETAINED_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
STOP_GAINED (genophenocorr.constants.variant_effects.VariantEffect attribute)
STOP_LOST (genophenocorr.constants.variant_effects.VariantEffect attribute)
STOP_RETAINED_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
store_annotations() (genophenocorr.preprocessing.ProteinAnnotationCache method)
(genophenocorr.preprocessing.VariantAnnotationCache method)
SYNONYMOUS_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
T
test() (genophenocorr.analysis.predicate.ExonPredicate method)
(genophenocorr.analysis.predicate.HPOPresentPredicate method)
(genophenocorr.analysis.predicate.PolyPredicate method)
(genophenocorr.analysis.predicate.ProtFeaturePredicate method)
(genophenocorr.analysis.predicate.ProtFeatureTypePredicate method)
(genophenocorr.analysis.predicate.SimplePredicate method)
(genophenocorr.analysis.predicate.VariantEffectPredicate method)
(genophenocorr.analysis.predicate.VariantPredicate method)
TF_BINDING_SITE_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
TFBS_ABLATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
TFBS_AMPLIFICATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
THREE_PRIME_UTR_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
total_patient_count (genophenocorr.model.Cohort property)
TRANSCRIPT_ABLATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
TRANSCRIPT_AMPLIFICATION (genophenocorr.constants.variant_effects.VariantEffect attribute)
transcript_id (genophenocorr.model.TranscriptAnnotation attribute)
(genophenocorr.model.TranscriptAnnotation property)
TranscriptAnnotation (class in genophenocorr.model)
tx_annotations (genophenocorr.model.Variant attribute)
(genophenocorr.model.Variant property)
U
UniprotProteinMetadataService (class in genophenocorr.preprocessing)
UPSTREAM_GENE_VARIANT (genophenocorr.constants.variant_effects.VariantEffect attribute)
V
VarCachingFunctionalAnnotator (class in genophenocorr.preprocessing)
Variant (class in genophenocorr.model)
variant_class (genophenocorr.model.Variant attribute)
(genophenocorr.model.Variant property)
variant_coordinates (genophenocorr.model.Variant attribute)
(genophenocorr.model.Variant property)
variant_effects (genophenocorr.model.TranscriptAnnotation attribute)
(genophenocorr.model.TranscriptAnnotation property)
variant_string (genophenocorr.model.Variant attribute)
(genophenocorr.model.Variant property)
VariantAnnotationCache (class in genophenocorr.preprocessing)
VariantCoordinateFinder (class in genophenocorr.preprocessing)
VariantCoordinates (class in genophenocorr.model)
VariantEffect (class in genophenocorr.constants.variant_effects)
VariantEffectPredicate (class in genophenocorr.analysis.predicate)
VariantPredicate (class in genophenocorr.analysis.predicate)
variants (genophenocorr.model.Patient attribute)
(genophenocorr.model.Patient property)
variants_table() (genophenocorr.view.CohortViewer method)
VepFunctionalAnnotator (class in genophenocorr.preprocessing)