anhima
Locating samples and variants
Genotypes
Allele frequencies
Site frequencies
Doubleton sharing
Linkage disequilibrium
Genetic distance
Principal components analysis
Multidimensional scaling
Trees
Pedigrees (families and crosses)
Input/output utilities
HDF5 utilities
Miscellaneous utilities
Simulations
anhima
Docs
»
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
I
|
L
|
M
|
N
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
A
allele_count() (in module anhima.af)
allele_counts() (in module anhima.af)
allele_frequencies() (in module anhima.af)
allele_frequency() (in module anhima.af)
allele_number() (in module anhima.af)
allelism() (in module anhima.af)
anhima (module)
anhima.af (module)
anhima.dist (module)
anhima.f2 (module)
anhima.gt (module)
anhima.h5 (module)
anhima.io (module)
anhima.ld (module)
anhima.loc (module)
anhima.mds (module)
anhima.pca (module)
anhima.ped (module)
anhima.sf (module)
anhima.sim (module)
anhima.tree (module)
anhima.util (module)
as_012() (in module anhima.gt)
as_allele_counts() (in module anhima.gt)
as_haplotypes() (in module anhima.gt)
as_n_alt() (in module anhima.gt)
B
bionj() (in module anhima.tree)
block_apply() (in module anhima.util)
block_compress2d() (in module anhima.util)
block_take2d() (in module anhima.util)
C
classical() (in module anhima.mds)
color_edges_by_group_majority() (in module anhima.tree)
compress_variants() (in module anhima.loc)
count_called() (in module anhima.gt)
count_diploid_mendelian_error() (in module anhima.ped)
count_doubletons() (in module anhima.af)
count_genotypes() (in module anhima.gt)
count_het() (in module anhima.gt)
count_hom() (in module anhima.gt)
count_hom_alt() (in module anhima.gt)
count_hom_ref() (in module anhima.gt)
count_missing() (in module anhima.gt)
count_non_segregating() (in module anhima.af)
count_non_variant() (in module anhima.af)
count_segregating() (in module anhima.af)
count_shared_doubletons() (in module anhima.f2)
count_singletons() (in module anhima.af)
count_variant() (in module anhima.af)
D
diploid_inheritance() (in module anhima.ped)
diploid_mendelian_error() (in module anhima.ped)
E
evenly_downsample_variants() (in module anhima.loc)
I
impute_inheritance_nearest() (in module anhima.ped)
inheritance_block_masks() (in module anhima.ped)
is_called() (in module anhima.gt)
is_doubleton() (in module anhima.af)
is_het() (in module anhima.gt)
is_hom() (in module anhima.gt)
is_hom_alt() (in module anhima.gt)
is_hom_ref() (in module anhima.gt)
is_missing() (in module anhima.gt)
is_non_segregating() (in module anhima.af)
is_non_variant() (in module anhima.af)
is_segregating() (in module anhima.af)
is_singleton() (in module anhima.af)
is_variant() (in module anhima.af)
L
ld_prune_pairwise() (in module anhima.ld)
load_region() (in module anhima.h5)
locate_interval() (in module anhima.loc)
locate_intervals() (in module anhima.loc)
locate_position() (in module anhima.loc)
locate_positions() (in module anhima.loc)
M
max_allele() (in module anhima.gt)
maximum_likelihood_ancestry() (in module anhima.af)
N
nj() (in module anhima.tree)
normalise_doubleton_counts() (in module anhima.f2)
P
pack_diploid() (in module anhima.gt)
pairwise_distance() (in module anhima.dist)
pairwise_genotype_ld() (in module anhima.ld)
pairwise_ld_decay() (in module anhima.ld)
pca() (in module anhima.pca)
plot_continuous_calldata() (in module anhima.gt)
plot_continuous_calldata_by_sample() (in module anhima.gt)
plot_coords() (in module anhima.mds)
(in module anhima.pca)
plot_diploid_genotypes() (in module anhima.gt)
plot_discrete_calldata() (in module anhima.gt)
plot_f2_fig() (in module anhima.f2)
plot_genotype_counts_by_sample() (in module anhima.gt)
plot_genotype_counts_by_variant() (in module anhima.gt)
plot_ld_decay_by_distance() (in module anhima.ld)
plot_ld_decay_by_separation() (in module anhima.ld)
plot_loadings() (in module anhima.pca)
plot_pairwise_distance() (in module anhima.dist)
plot_pairwise_ld() (in module anhima.ld)
plot_phylo() (in module anhima.tree)
plot_shared_doubletons() (in module anhima.f2)
plot_site_frequency_spectrum() (in module anhima.sf)
plot_total_doubletons() (in module anhima.f2)
plot_variance_explained() (in module anhima.pca)
plot_variant_locator() (in module anhima.loc)
plot_windowed_genotype_counts() (in module anhima.gt)
plot_windowed_genotype_density() (in module anhima.gt)
plot_windowed_genotype_rate() (in module anhima.gt)
plot_windowed_ld() (in module anhima.ld)
plot_windowed_variant_counts() (in module anhima.loc)
plot_windowed_variant_density() (in module anhima.loc)
Q
query_variants() (in module anhima.loc)
R
randomly_downsample_variants() (in module anhima.loc)
read_tree() (in module anhima.tree)
S
save_tped() (in module anhima.h5)
(in module anhima.io)
simulate_biallelic_genotypes() (in module anhima.sim)
simulate_genotypes_with_ld() (in module anhima.sim)
simulate_relatedness() (in module anhima.sim)
site_frequency_spectrum() (in module anhima.sf)
site_frequency_spectrum_folded() (in module anhima.sf)
site_frequency_spectrum_folded_scaled() (in module anhima.sf)
site_frequency_spectrum_scaled() (in module anhima.sf)
smacof() (in module anhima.mds)
T
tabulate_inheritance_blocks() (in module anhima.ped)
tabulate_inheritance_switches() (in module anhima.ped)
take2d_pointsel() (in module anhima.h5)
take_samples() (in module anhima.loc)
take_variants() (in module anhima.loc)
U
unpack_diploid() (in module anhima.gt)
V
view_interval() (in module anhima.loc)
view_position() (in module anhima.loc)
view_sample() (in module anhima.loc)
W
windowed_genotype_counts() (in module anhima.gt)
windowed_genotype_density() (in module anhima.gt)
windowed_genotype_rate() (in module anhima.gt)
windowed_ld_decay() (in module anhima.ld)
windowed_statistic() (in module anhima.loc)
windowed_variant_counts() (in module anhima.loc)
windowed_variant_density() (in module anhima.loc)
write_tree() (in module anhima.tree)
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
htmlzip
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.