scikit-allel
Data structures
GenotypeArray
HaplotypeArray
AlleleCountsArray
VariantTable
FeatureTable
SortedIndex
UniqueIndex
SortedMultiIndex
Compressed arrays (bcolz)
GenotypeCArray
HaplotypeCArray
AlleleCountsCArray
VariantCTable
FeatureCTable
Utility functions
Statistics
Diversity & divergence
Pairwise distance
Hardy-Weinberg equilibrium
Window utilities
Plotting functions
Pairwise distance
scikit-allel
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Index
A
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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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Q
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S
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T
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U
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V
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W
A
allel (module)
allel.bcolz (module)
allel.model (module)
allel.plot (module)
allel.stats (module)
AlleleCountsArray (class in allel.model)
AlleleCountsCArray (class in allel.bcolz)
allelism() (allel.model.AlleleCountsArray method)
C
carray_block_compress() (in module allel.bcolz)
carray_block_map() (in module allel.bcolz)
carray_block_max() (in module allel.bcolz)
carray_block_min() (in module allel.bcolz)
carray_block_sum() (in module allel.bcolz)
carray_block_take() (in module allel.bcolz)
carray_from_hdf5() (in module allel.bcolz)
count_alleles() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_alleles_subpops() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_alt() (allel.model.HaplotypeArray method)
count_call() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_called() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
count_doubleton() (allel.model.AlleleCountsArray 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)
(allel.model.HaplotypeArray method)
count_non_segregating() (allel.model.AlleleCountsArray method)
count_non_variant() (allel.model.AlleleCountsArray method)
count_ref() (allel.model.HaplotypeArray method)
count_segregating() (allel.model.AlleleCountsArray method)
count_singleton() (allel.model.AlleleCountsArray method)
count_variant() (allel.model.AlleleCountsArray method)
ctable_block_compress() (in module allel.bcolz)
ctable_block_take() (in module allel.bcolz)
ctable_from_hdf5_group() (in module allel.bcolz)
E
eval() (allel.model.FeatureTable method)
(allel.model.VariantTable method)
F
FeatureCTable (class in allel.bcolz)
FeatureTable (class in allel.model)
from_gff3() (allel.model.FeatureTable static method)
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)
GenotypeCArray (class in allel.bcolz)
H
haploidify_samples() (allel.model.GenotypeArray method)
HaplotypeArray (class in allel.model)
HaplotypeCArray (class in allel.bcolz)
heterozygosity_expected() (in module allel.stats)
heterozygosity_observed() (in module allel.stats)
I
inbreeding_coefficient() (in module allel.stats)
intersect() (allel.model.SortedIndex method)
(allel.model.UniqueIndex method)
intersect_range() (allel.model.SortedIndex method)
intersect_ranges() (allel.model.SortedIndex method)
is_alt() (allel.model.HaplotypeArray method)
is_call() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
is_called() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
is_doubleton() (allel.model.AlleleCountsArray 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)
(allel.model.HaplotypeArray method)
is_non_segregating() (allel.model.AlleleCountsArray method)
is_non_variant() (allel.model.AlleleCountsArray method)
is_ref() (allel.model.HaplotypeArray method)
is_segregating() (allel.model.AlleleCountsArray method)
is_singleton() (allel.model.AlleleCountsArray method)
is_unique (allel.model.SortedIndex attribute)
is_variant() (allel.model.AlleleCountsArray method)
L
locate_intersection() (allel.model.SortedIndex method)
(allel.model.UniqueIndex method)
locate_intersection_ranges() (allel.model.SortedIndex method)
locate_key() (allel.model.SortedIndex method)
(allel.model.SortedMultiIndex method)
(allel.model.UniqueIndex method)
locate_keys() (allel.model.SortedIndex method)
(allel.model.UniqueIndex method)
locate_range() (allel.model.SortedIndex method)
(allel.model.SortedMultiIndex method)
locate_ranges() (allel.model.SortedIndex method)
M
mean_pairwise_divergence() (in module allel.stats)
mean_pairwise_diversity() (in module allel.stats)
moving_statistic() (in module allel.stats)
N
n_alleles (allel.model.AlleleCountsArray attribute)
n_features (allel.model.FeatureTable attribute)
n_haplotypes (allel.model.HaplotypeArray attribute)
n_samples (allel.model.GenotypeArray attribute)
n_variants (allel.model.AlleleCountsArray attribute)
(allel.model.GenotypeArray attribute)
(allel.model.HaplotypeArray attribute)
(allel.model.VariantTable attribute)
names (allel.model.FeatureTable attribute)
(allel.model.VariantTable attribute)
P
pairwise_distance() (in module allel.plot)
(in module allel.stats)
pairwise_dxy() (in module allel.stats)
per_base() (in module allel.stats)
ploidy (allel.model.GenotypeArray attribute)
Q
query() (allel.model.FeatureTable method)
(allel.model.VariantTable method)
query_position() (allel.model.VariantTable method)
query_region() (allel.model.VariantTable method)
S
sequence_divergence() (in module allel.stats)
sequence_diversity() (in module allel.stats)
SortedIndex (class in allel.model)
SortedMultiIndex (class in allel.model)
subset() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
T
to_allele_counts() (allel.model.GenotypeArray method)
to_frequencies() (allel.model.AlleleCountsArray method)
to_genotypes() (allel.model.HaplotypeArray method)
to_gt() (allel.model.GenotypeArray method)
to_haplotypes() (allel.model.GenotypeArray method)
to_mask() (allel.model.FeatureTable method)
to_n_alt() (allel.model.GenotypeArray method)
to_packed() (allel.model.GenotypeArray method)
to_sparse() (allel.model.GenotypeArray method)
(allel.model.HaplotypeArray method)
to_vcf() (allel.model.VariantTable method)
U
UniqueIndex (class in allel.model)
V
VariantCTable (class in allel.bcolz)
VariantTable (class in allel.model)
W
windowed_count() (in module allel.stats)
windowed_divergence() (in module allel.stats)
windowed_diversity() (in module allel.stats)
windowed_statistic() (in module allel.stats)
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