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A
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B
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C
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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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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
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Z
A
add_cn_samples() (in module pypgx.sdk.utils)
AlleleNotFoundError
Archive (class in pypgx.sdk.utils)
B
build_definition_table() (in module pypgx.api.core)
BundleNotFoundError
C
call_genotypes() (in module pypgx.api.genotype)
call_phenotypes() (in module pypgx.api.utils)
check_metadata() (pypgx.sdk.utils.Archive method)
check_type() (pypgx.sdk.utils.Archive method)
collapse_alleles() (in module pypgx.api.core)
combine_results() (in module pypgx.api.utils)
compare_genotypes() (in module pypgx.api.utils)
compare_metadata() (in module pypgx.sdk.utils)
compute_control_statistics() (in module pypgx.api.utils)
compute_copy_number() (in module pypgx.api.utils)
compute_target_depth() (in module pypgx.api.utils)
copy_metadata() (pypgx.sdk.utils.Archive method)
count_alleles() (in module pypgx.api.utils)
create_consolidated_vcf() (in module pypgx.api.utils)
create_input_vcf() (in module pypgx.api.utils)
create_regions_bed() (in module pypgx.api.utils)
CYP2A6Genotyper (class in pypgx.api.genotype)
CYP2B6Genotyper (class in pypgx.api.genotype)
CYP2D6Genotyper (class in pypgx.api.genotype)
CYP2E1Genotyper (class in pypgx.api.genotype)
CYP4F2Genotyper (class in pypgx.api.genotype)
E
estimate_phase_beagle() (in module pypgx.api.utils)
F
filter_samples() (in module pypgx.api.utils)
from_file() (pypgx.sdk.utils.Archive class method)
G
G6PDGenotyper (class in pypgx.api.genotype)
GeneNotFoundError
get_bundle_path() (in module pypgx.sdk.utils)
get_default_allele() (in module pypgx.api.core)
get_exon_ends() (in module pypgx.api.core)
get_exon_starts() (in module pypgx.api.core)
get_function() (in module pypgx.api.core)
get_paralog() (in module pypgx.api.core)
get_priority() (in module pypgx.api.core)
get_recommendation() (in module pypgx.api.core)
get_ref_allele() (in module pypgx.api.core)
get_region() (in module pypgx.api.core)
get_score() (in module pypgx.api.core)
get_strand() (in module pypgx.api.core)
get_variant_impact() (in module pypgx.api.core)
get_variant_synonyms() (in module pypgx.api.core)
GSTM1Genotyper (class in pypgx.api.genotype)
GSTT1Genotyper (class in pypgx.api.genotype)
H
has_phenotype() (in module pypgx.api.core)
has_score() (in module pypgx.api.core)
has_sv() (in module pypgx.api.core)
I
import_read_depth() (in module pypgx.api.utils)
import_variants() (in module pypgx.api.utils)
IncorrectMetadataError
IncorrectSemanticTypeError
is_legit_allele() (in module pypgx.api.core)
is_target_gene() (in module pypgx.api.core)
L
list_alleles() (in module pypgx.api.core)
list_functions() (in module pypgx.api.core)
list_genes() (in module pypgx.api.core)
list_phenotypes() (in module pypgx.api.core)
list_variants() (in module pypgx.api.core)
load_allele_table() (in module pypgx.api.core)
load_cnv_table() (in module pypgx.api.core)
load_cpic_table() (in module pypgx.api.core)
load_diplotype_table() (in module pypgx.api.core)
load_equation_table() (in module pypgx.api.core)
load_gene_table() (in module pypgx.api.core)
load_phenotype_table() (in module pypgx.api.core)
load_recommendation_table() (in module pypgx.api.core)
load_variant_table() (in module pypgx.api.core)
M
module
pypgx.api.core
pypgx.api.genotype
pypgx.api.pipeline
pypgx.api.plot
pypgx.api.utils
pypgx.sdk.utils
N
NotTargetGeneError
P
parse_pharmvar() (in module pypgx.sdk.utils)
PhenotypeNotFoundError
plot_bam_copy_number() (in module pypgx.api.plot)
plot_bam_read_depth() (in module pypgx.api.plot)
plot_cn_af() (in module pypgx.api.plot)
plot_vcf_allele_fraction() (in module pypgx.api.plot)
plot_vcf_read_depth() (in module pypgx.api.plot)
predict_alleles() (in module pypgx.api.utils)
predict_cnv() (in module pypgx.api.utils)
predict_phenotype() (in module pypgx.api.core)
predict_score() (in module pypgx.api.core)
prepare_depth_of_coverage() (in module pypgx.api.utils)
print_data() (in module pypgx.api.utils)
print_metadata() (in module pypgx.api.utils)
pypgx.api.core
module
pypgx.api.genotype
module
pypgx.api.pipeline
module
pypgx.api.plot
module
pypgx.api.utils
module
pypgx.sdk.utils
module
R
run_chip_pipeline() (in module pypgx.api.pipeline)
run_long_read_pipeline() (in module pypgx.api.pipeline)
run_ngs_pipeline() (in module pypgx.api.pipeline)
S
SemanticTypeNotFoundError
SimpleGenotyper (class in pypgx.api.genotype)
simulate_copy_number() (in module pypgx.sdk.utils)
SLC22A2Genotyper (class in pypgx.api.genotype)
slice_bam() (in module pypgx.api.utils)
sort_alleles() (in module pypgx.api.core)
SULT1A1Genotyper (class in pypgx.api.genotype)
T
test_cnv_caller() (in module pypgx.api.utils)
to_file() (pypgx.sdk.utils.Archive method)
train_cnv_caller() (in module pypgx.api.utils)
type (pypgx.sdk.utils.Archive property)
U
UGT1A4Genotyper (class in pypgx.api.genotype)
UGT2B15Genotyper (class in pypgx.api.genotype)
UGT2B17Genotyper (class in pypgx.api.genotype)
V
VariantNotFoundError
Z
zipdir() (in module pypgx.sdk.utils)
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