scikit-allel
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
Pairwise distance
Hardy-Weinberg equilibrium
Linkage disequilibrium
Window utilities
Plotting functions
Variant location
Pairwise distance
Linkage disequilibrium
scikit-allel
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