Index

A

alt_ref (sistem.Parameters attribute) alter_prop (sistem.Parameters attribute)

arm_rate (sistem.Parameters attribute) arm_ratios (sistem.Parameters attribute)

B

BaseAnatomy (class in sistem.anatomy)

BaseLibrary (class in sistem.selection) bin_size (sistem.Parameters attribute)

C

capacities (sistem.Parameters attribute) check_viability() (sistem.selection.BaseLibrary method) chrom_dup_rate (sistem.Parameters attribute) chrom_lens (sistem.Parameters attribute) chrom_names (sistem.Parameters attribute) chromosomal_rate (sistem.Parameters attribute)

clones (sistem.GrowthSimulator attribute) CN_coeff (sistem.Parameters attribute) compute_fitness() (sistem.selection.BaseLibrary method) coverage (sistem.Parameters attribute) create_random_metastatic_libraries() (sistem.anatomy.BaseAnatomy method) cycle_gen() (sistem.GrowthSimulator method)

D

dists (sistem.anatomy.BaseAnatomy attribute)

E

EG_r (sistem.Parameters attribute)

epsilon (sistem.Parameters attribute) exp_pop (sistem.anatomy.BaseAnatomy attribute)

F

FittedArmLibrary (class in sistem.selection) FittedHybridLibrary (class in sistem.selection) FittedRegionLibrary (class in sistem.selection)

focal_driver_rate (sistem.Parameters attribute) focal_gain_rate (sistem.Parameters attribute) focal_pass_rate (sistem.Parameters attribute)

G

gen (sistem.GrowthSimulator attribute) gen_readcounts_bulk() (in module sistem.data) gen_readcounts_singlecell() (in module sistem.data) gen_reads() (in module sistem.data) GenotypeAnatomy (class in sistem.anatomy) get_driver_start_regions() (sistem.selection.BaseLibrary method) get_oneway_transition_probabilities() (sistem.anatomy.BaseAnatomy method) (sistem.anatomy.GenotypeAnatomy method) (sistem.anatomy.SimpleAnatomy method) (sistem.anatomy.StaticAnatomy method)

get_passenger_start_regions() (sistem.selection.BaseLibrary method) get_total_transition_probability() (sistem.anatomy.BaseAnatomy method) (sistem.anatomy.GenotypeAnatomy method) (sistem.anatomy.SimpleAnatomy method) (sistem.anatomy.StaticAnatomy method) growth_rate (sistem.Parameters attribute) GrowthSimulator (class in sistem)

I

init_attributes() (sistem.selection.BaseLibrary method) init_base_fit() (sistem.selection.BaseLibrary method) init_max_fit() (sistem.selection.BaseLibrary method) initialize() (sistem.selection.BaseLibrary method) (sistem.selection.FittedArmLibrary method) (sistem.selection.FittedHybridLibrary method) (sistem.selection.FittedRegionLibrary method) (sistem.selection.RandomArmLibrary method) (sistem.selection.RandomHybridLibrary method) (sistem.selection.RandomRegionLibrary method)

initialize_distances() (sistem.anatomy.BaseAnatomy method) (sistem.anatomy.StaticAnatomy method) is_driver_region_model (sistem.selection.BaseLibrary attribute) is_driver_SNV_model (sistem.selection.BaseLibrary attribute)

L

length_mean (sistem.Parameters attribute) lifespan_mean (sistem.Parameters attribute)

log_path (sistem.Parameters attribute) lorenz_y (sistem.Parameters attribute)

M

mag_mean (sistem.Parameters attribute) max_distinct_driv_ratio (sistem.Parameters attribute) max_growth_rate_multiplier (sistem.Parameters attribute) max_ploidy (sistem.Parameters attribute)

max_region_CN (sistem.Parameters attribute) max_region_SNV (sistem.Parameters attribute) min_detectable (sistem.Parameters attribute) min_mut_fraction (sistem.Parameters attribute) min_ploidy (sistem.Parameters attribute)

N

N0 (sistem.Parameters attribute) ncells_meta (sistem.Parameters attribute) ncells_normal (sistem.Parameters attribute)

ncells_prim (sistem.Parameters attribute) num_chrom (sistem.Parameters attribute) num_processors (sistem.Parameters attribute)

O

OG_r (sistem.Parameters attribute)

out_dir (sistem.Parameters attribute)

P

Parameters (class in sistem)

points (sistem.anatomy.BaseAnatomy attribute)

R

RandomArmLibrary (class in sistem.selection) RandomHybridLibrary (class in sistem.selection) RandomRegionLibrary (class in sistem.selection)

read_len (sistem.Parameters attribute) ref (sistem.Parameters attribute) region_len (sistem.Parameters attribute)

S

sample_cells() (sistem.GrowthSimulator method) save_checkpoint() (sistem.GrowthSimulator method) seq_error (sistem.Parameters attribute) SimpleAnatomy (class in sistem.anatomy) simulate_agents() (sistem.GrowthSimulator method) simulate_clonal_lineage() (sistem.GrowthSimulator method)

simulate_singlecell_lineage() (sistem.GrowthSimulator method) site_counts (sistem.GrowthSimulator attribute) SNV_coeff (sistem.Parameters attribute) SNV_driver_rate (sistem.Parameters attribute) SNV_pass_rate (sistem.Parameters attribute) StaticAnatomy (class in sistem.anatomy)

T

t_max (sistem.Parameters attribute)

TSG_r (sistem.Parameters attribute)

U

update_stats() (sistem.selection.BaseLibrary method)

W

WGD_rate (sistem.Parameters attribute)