scikit-allel
Data structures
GenotypeArray
HaplotypeArray
PositionIndex
LabelIndex
Statistics
Windowed statistics
scikit-allel
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Index
A
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C
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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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T
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V
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W
A
allel (module)
allel.model (module)
allel.stats (module)
allele_count() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
allele_counts() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
allele_frequencies() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
allele_frequency() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
allele_number() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
allelism() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
C
count_call() (allel.model.GenotypeArray method)
count_called() (allel.model.GenotypeArray method)
count_doubleton() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_het() (allel.model.GenotypeArray method)
count_hom() (allel.model.GenotypeArray method)
count_hom_alt() (allel.model.GenotypeArray method)
count_hom_ref() (allel.model.GenotypeArray method)
count_missing() (allel.model.GenotypeArray method)
count_non_segregating() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_non_variant() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_segregating() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_singleton() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_variant() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
F
from_packed() (allel.model.GenotypeArray static method)
from_sparse() (allel.model.GenotypeArray static method)
(allel.model.HaplotypeArray static method)
G
GenotypeArray (class in allel.model)
H
haploidify_samples() (allel.model.GenotypeArray method)
HaplotypeArray (class in allel.model)
heterozygosity_expected() (allel.model.GenotypeArray method)
heterozygosity_observed() (allel.model.GenotypeArray method)
I
inbreeding_coefficient() (allel.model.GenotypeArray method)
intersect() (allel.model.LabelIndex method)
(allel.model.PositionIndex method)
intersect_range() (allel.model.PositionIndex method)
intersect_ranges() (allel.model.PositionIndex method)
is_call() (allel.model.GenotypeArray method)
is_called() (allel.model.GenotypeArray method)
is_doubleton() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
is_het() (allel.model.GenotypeArray method)
is_hom() (allel.model.GenotypeArray method)
is_hom_alt() (allel.model.GenotypeArray method)
is_hom_ref() (allel.model.GenotypeArray method)
is_missing() (allel.model.GenotypeArray method)
is_non_segregating() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
is_non_variant() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
is_segregating() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
is_singleton() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
is_unique (allel.model.PositionIndex attribute)
is_variant() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
L
LabelIndex (class in allel.model)
locate_intersection() (allel.model.LabelIndex method)
(allel.model.PositionIndex method)
locate_intersection_ranges() (allel.model.PositionIndex method)
locate_key() (allel.model.LabelIndex method)
(allel.model.PositionIndex method)
locate_keys() (allel.model.LabelIndex method)
(allel.model.PositionIndex method)
locate_range() (allel.model.PositionIndex method)
locate_ranges() (allel.model.PositionIndex method)
M
mean_pairwise_difference() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
N
n_haplotypes (allel.model.HaplotypeArray attribute)
n_samples (allel.model.GenotypeArray attribute)
n_variants (allel.model.GenotypeArray attribute)
(allel.model.HaplotypeArray attribute)
P
ploidy (allel.model.GenotypeArray attribute)
PositionIndex (class in allel.model)
T
to_allele_counts() (allel.model.GenotypeArray method)
to_n_alt() (allel.model.GenotypeArray method)
to_packed() (allel.model.GenotypeArray method)
to_sparse() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
V
view_genotypes() (allel.model.HaplotypeArray method)
view_haplotypes() (allel.model.GenotypeArray method)
W
windowed_mean_per_base() (in module allel.stats)
windowed_nnz() (in module allel.stats)
windowed_nnz_per_base() (in module allel.stats)
windowed_nucleotide_diversity() (in module allel.stats)
windowed_statistic() (in module allel.stats)
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