scikit-allel
Data structures
In-memory data structures
GenotypeArray
HaplotypeArray
AlleleCountsArray
VariantTable
FeatureTable
SortedIndex
UniqueIndex
SortedMultiIndex
Utility functions
Compressed arrays (bcolz)
GenotypeCArray
HaplotypeCArray
AlleleCountsCArray
VariantCTable
FeatureCTable
Utility functions
Statistics
Diversity & divergence
F-statistics
Hardy-Weinberg equilibrium
Linkage disequilibrium
Pairwise distance and ordination
Principal components analysis
Admixture tests
Window utilities
Preprocessing utilities
Plotting functions
Variant location
Pairwise distance
Linkage disequilibrium
Input/output utilities
Release notes
v0.15
v0.14
v0.12
v0.11
v0.10
v0.9
v0.8
v0.7
v0.6
scikit-allel
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Index
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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Q
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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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W
A
allel (module)
allel.io (module)
allel.model.bcolz (module)
allel.model.ndarray (module)
allel.plot (module)
allel.stats.admixture (module)
allel.stats.decomposition (module)
allel.stats.distance (module)
allel.stats.diversity (module)
allel.stats.fst (module)
allel.stats.hw (module)
allel.stats.ld (module)
allel.stats.preprocessing (module)
allel.stats.window (module)
AlleleCountsArray (class in allel.model.ndarray)
AlleleCountsCArray (class in allel.model.bcolz)
allelism() (allel.model.ndarray.AlleleCountsArray method)
B
blockwise_hudson_fst() (in module allel.stats.fst)
blockwise_patterson_d() (in module allel.stats.admixture)
blockwise_patterson_f3() (in module allel.stats.admixture)
blockwise_patterson_fst() (in module allel.stats.fst)
blockwise_weir_cockerham_fst() (in module allel.stats.fst)
C
carray_block_compress() (in module allel.model.bcolz)
carray_block_map() (in module allel.model.bcolz)
carray_block_max() (in module allel.model.bcolz)
carray_block_min() (in module allel.model.bcolz)
carray_block_sum() (in module allel.model.bcolz)
carray_block_take() (in module allel.model.bcolz)
carray_from_hdf5() (in module allel.model.bcolz)
carray_to_hdf5() (in module allel.model.bcolz)
CenterScaler (class in allel.stats.preprocessing)
condensed_coords() (in module allel.stats.distance)
condensed_coords_between() (in module allel.stats.distance)
condensed_coords_within() (in module allel.stats.distance)
count_alleles() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
count_alleles_subpops() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
count_alt() (allel.model.ndarray.HaplotypeArray method)
count_call() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
count_called() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
count_doubleton() (allel.model.ndarray.AlleleCountsArray method)
count_het() (allel.model.ndarray.GenotypeArray method)
count_hom() (allel.model.ndarray.GenotypeArray method)
count_hom_alt() (allel.model.ndarray.GenotypeArray method)
count_hom_ref() (allel.model.ndarray.GenotypeArray method)
count_missing() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
count_non_segregating() (allel.model.ndarray.AlleleCountsArray method)
count_non_variant() (allel.model.ndarray.AlleleCountsArray method)
count_ref() (allel.model.ndarray.HaplotypeArray method)
count_segregating() (allel.model.ndarray.AlleleCountsArray method)
count_singleton() (allel.model.ndarray.AlleleCountsArray method)
count_variant() (allel.model.ndarray.AlleleCountsArray method)
create_allele_mapping() (in module allel.model.ndarray)
ctable_block_compress() (in module allel.model.bcolz)
ctable_block_take() (in module allel.model.bcolz)
ctable_from_hdf5_group() (in module allel.model.bcolz)
ctable_to_hdf5_group() (in module allel.model.bcolz)
E
eval() (allel.model.ndarray.FeatureTable method)
(allel.model.ndarray.VariantTable method)
F
FeatureCTable (class in allel.model.bcolz)
FeatureTable (class in allel.model.ndarray)
fill_masked() (allel.model.ndarray.GenotypeArray method)
from_gff3() (allel.model.ndarray.FeatureTable static method)
from_packed() (allel.model.ndarray.GenotypeArray static method)
from_sparse() (allel.model.ndarray.GenotypeArray static method)
(allel.model.ndarray.HaplotypeArray static method)
G
GenotypeArray (class in allel.model.ndarray)
GenotypeCArray (class in allel.model.bcolz)
get_scaler() (in module allel.stats.preprocessing)
H
haploidify_samples() (allel.model.ndarray.GenotypeArray method)
HaplotypeArray (class in allel.model.ndarray)
HaplotypeCArray (class in allel.model.bcolz)
heterozygosity_expected() (in module allel.stats.hw)
heterozygosity_observed() (in module allel.stats.hw)
hudson_fst() (in module allel.stats.fst)
I
inbreeding_coefficient() (in module allel.stats.hw)
intersect() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.UniqueIndex method)
intersect_range() (allel.model.ndarray.SortedIndex method)
intersect_ranges() (allel.model.ndarray.SortedIndex method)
is_alt() (allel.model.ndarray.HaplotypeArray method)
is_call() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
is_called() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
is_doubleton() (allel.model.ndarray.AlleleCountsArray method)
is_het() (allel.model.ndarray.GenotypeArray method)
is_hom() (allel.model.ndarray.GenotypeArray method)
is_hom_alt() (allel.model.ndarray.GenotypeArray method)
is_hom_ref() (allel.model.ndarray.GenotypeArray method)
is_missing() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
is_non_segregating() (allel.model.ndarray.AlleleCountsArray method)
is_non_variant() (allel.model.ndarray.AlleleCountsArray method)
is_ref() (allel.model.ndarray.HaplotypeArray method)
is_segregating() (allel.model.ndarray.AlleleCountsArray method)
is_singleton() (allel.model.ndarray.AlleleCountsArray method)
is_unique (allel.model.ndarray.SortedIndex attribute)
is_variant() (allel.model.ndarray.AlleleCountsArray method)
iter_gff3() (in module allel.io)
L
locate_fixed_differences() (in module allel.model.ndarray)
locate_intersection() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.UniqueIndex method)
locate_intersection_ranges() (allel.model.ndarray.SortedIndex method)
locate_key() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.SortedMultiIndex method)
(allel.model.ndarray.UniqueIndex method)
locate_keys() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.UniqueIndex method)
locate_private_alleles() (in module allel.model.ndarray)
locate_range() (allel.model.ndarray.SortedIndex method)
(allel.model.ndarray.SortedMultiIndex method)
locate_ranges() (allel.model.ndarray.SortedIndex method)
locate_unlinked() (in module allel.stats.ld)
M
map_alleles() (allel.model.ndarray.AlleleCountsArray method)
(allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
mask (allel.model.ndarray.GenotypeArray attribute)
max_allele() (allel.model.ndarray.AlleleCountsArray method)
mean_pairwise_difference() (in module allel.stats.diversity)
mean_pairwise_difference_between() (in module allel.stats.diversity)
moving_statistic() (in module allel.stats.window)
N
n_alleles (allel.model.ndarray.AlleleCountsArray attribute)
n_features (allel.model.ndarray.FeatureTable attribute)
n_haplotypes (allel.model.ndarray.HaplotypeArray attribute)
n_samples (allel.model.ndarray.GenotypeArray attribute)
n_variants (allel.model.ndarray.AlleleCountsArray attribute)
(allel.model.ndarray.GenotypeArray attribute)
(allel.model.ndarray.HaplotypeArray attribute)
(allel.model.ndarray.VariantTable attribute)
names (allel.model.ndarray.FeatureTable attribute)
(allel.model.ndarray.VariantTable attribute)
P
pairwise_distance() (in module allel.plot)
(in module allel.stats.distance)
pairwise_dxy() (in module allel.stats.distance)
pairwise_ld() (in module allel.plot)
patterson_d() (in module allel.stats.admixture)
patterson_f2() (in module allel.stats.admixture)
patterson_f3() (in module allel.stats.admixture)
patterson_fst() (in module allel.stats.fst)
PattersonScaler (class in allel.stats.preprocessing)
pca() (in module allel.stats.decomposition)
pcoa() (in module allel.stats.distance)
per_base() (in module allel.stats.window)
ploidy (allel.model.ndarray.GenotypeArray attribute)
Q
query() (allel.model.ndarray.FeatureTable method)
(allel.model.ndarray.VariantTable method)
query_position() (allel.model.ndarray.VariantTable method)
query_region() (allel.model.ndarray.VariantTable method)
R
randomized_pca() (in module allel.stats.decomposition)
rogers_huff_r() (in module allel.stats.ld)
S
sequence_divergence() (in module allel.stats.diversity)
sequence_diversity() (in module allel.stats.diversity)
SortedIndex (class in allel.model.ndarray)
SortedMultiIndex (class in allel.model.ndarray)
StandardScaler (class in allel.stats.preprocessing)
subset() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
T
tajima_d() (in module allel.stats.diversity)
to_allele_counts() (allel.model.ndarray.GenotypeArray method)
to_frequencies() (allel.model.ndarray.AlleleCountsArray method)
to_genotypes() (allel.model.ndarray.HaplotypeArray method)
to_gt() (allel.model.ndarray.GenotypeArray method)
to_haplotypes() (allel.model.ndarray.GenotypeArray method)
to_mask() (allel.model.ndarray.FeatureTable method)
to_n_alt() (allel.model.ndarray.GenotypeArray method)
to_n_ref() (allel.model.ndarray.GenotypeArray method)
to_packed() (allel.model.ndarray.GenotypeArray method)
to_sparse() (allel.model.ndarray.GenotypeArray method)
(allel.model.ndarray.HaplotypeArray method)
to_vcf() (allel.model.ndarray.VariantTable method)
U
UniqueIndex (class in allel.model.ndarray)
V
variant_locator() (in module allel.plot)
VariantCTable (class in allel.model.bcolz)
VariantTable (class in allel.model.ndarray)
W
watterson_theta() (in module allel.stats.diversity)
weir_cockerham_fst() (in module allel.stats.fst)
windowed_count() (in module allel.stats.window)
windowed_df() (in module allel.stats.diversity)
windowed_divergence() (in module allel.stats.diversity)
windowed_diversity() (in module allel.stats.diversity)
windowed_hudson_fst() (in module allel.stats.fst)
windowed_patterson_fst() (in module allel.stats.fst)
windowed_r_squared() (in module allel.stats.ld)
windowed_statistic() (in module allel.stats.window)
windowed_tajima_d() (in module allel.stats.diversity)
windowed_watterson_theta() (in module allel.stats.diversity)
windowed_weir_cockerham_fst() (in module allel.stats.fst)
write_fasta() (in module allel.io)
write_vcf() (in module allel.io)
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