scikit-allel
v0.16.2
Data structures
Statistics
Plotting functions
Input/output utilities
Release notes
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
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X
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.selection (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
ehh_decay() (in module allel.stats.selection)
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
ihs() (in module allel.stats.selection)
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)
voight_painting() (in module allel.plot)
(in module allel.stats.selection)
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)
X
xpehh() (in module allel.stats.selection)
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