Index

A

annotate_vars() (in module mito.pp)

AOC() (in module mito.ut)

B

bootstrap_MiTo() (in module mito.tl)

build_tree() (in module mito.tl)

C

calculate_corr_distances() (in module mito.ut) call_genotypes() (in module mito.pp) CI() (in module mito.ut) clonal_inference() (mito.tl.MiToTreeAnnotator method) coarse_grained_tree() (in module mito.tl) compute_cell_fitness() (mito.tl.MiToTreeAnnotator method)

compute_clonal_fate_bias() (in module mito.tl) compute_distances() (in module mito.pp) compute_expansions() (mito.tl.MiToTreeAnnotator method) compute_lineage_biases() (in module mito.pp) compute_scPlasticity() (in module mito.tl) custom_ARI() (in module mito.ut)

D

distance_AUPRC() (in module mito.ut)

draw_embedding() (in module mito.pl)

E

extract_mut_order() (mito.tl.MiToTreeAnnotator method)

F

filter_afm() (in module mito.pp) filter_baseline() (in module mito.pp)

filter_cell_clones() (in module mito.pp) filter_cells() (in module mito.pp) filter_MiTo() (in module mito.pp)

G

genotype_mix() (in module mito.ut)

get_M() (mito.tl.MiToTreeAnnotator method) get_T() (mito.tl.MiToTreeAnnotator method)

H

heatmap_distances() (in module mito.pl)

heatmap_variants() (in module mito.pl)

I

infer_clones() (mito.tl.MiToTreeAnnotator method)

K

kbet() (in module mito.ut)

kNN_graph() (in module mito.pp)

M

make_afm() (in module mito.io) mito.io module mito.pl module mito.pp module mito.tl module mito.ut module

MiToTreeAnnotator (class in mito.tl) module mito.io mito.pl mito.pp mito.tl mito.ut MT_coverage_by_gene_polar() (in module mito.pl) MT_coverage_polar() (in module mito.pl) mut_profile() (in module mito.pl)

N

nb_regression() (in module mito.tl)

NN_entropy() (in module mito.ut)

P

packed_circle_plot() (in module mito.pl)

plot_ncells_nAD() (in module mito.pl) plot_tree() (in module mito.pl)

R

read_coverage() (in module mito.io) read_newick() (in module mito.io)

reduce_dimensions() (in module mito.pp) resolve_ambiguous_clones() (mito.tl.MiToTreeAnnotator method) RI() (in module mito.ut)

S

subsample_afm() (in module mito.ut)

V

vars_AF_spectrum() (in module mito.pl)

W

write_newick() (in module mito.io)