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Run simulation

tumopp() make_args()
Run tumopp

Phylogeny

make_igraph() subtree() internal_nodes()
Functions depending on igraph
propagate_drivers()
Functions to deal with driver mutations

Sampling

sample_uniform_regions() sample_random_regions() sample_bulk() evaluate_mrs() distances_mrs()
Sample cells from a population
dist_genealogy() dist_vaf() pairwise_distances()
Calculate genetic distance from genealogy or VAF
make_vaf() make_longer_vaf() longer_vaf() filter_detectable() sort_vaf()
Utilities for variant allele frequency
make_sample()
Sprinkle mutations on genealogy
fst() gst() pairwise_fst()
Calculate F_ST from matrix
combn_ids() summarize_capture_rate()
Sample cells from a population

Demography

extract_history() summarize_demography()
Functions for event history
filter_extant() count_extant() filter_common_ancestors()
Functions to modify population data.frame

Summary stats

math_score()
Evaluate heterogeneity
genetic_stats() morphological_stats()
Summarizing functions
stats_dispersion() summary_row() mutate_chisq() rpois_dispersion() tibble_dchisq()
Utilities for dispersion summary_row() and mutate_chisq() calculate various dispersion stats. stats_dispersion() is a shortcut to call them both at once.

Coordinate system

max_abs_xyz() dist_euclidean() transform_rotate()
Utilities for coordinate values
trans_coord_hex()
Transform coordinates into hexagonal grid
add_surface() add_phi()
Extract surface cells with mathematical morphology
as_cuboid() as.data.frame(<cuboid>) as.array(<cuboid>)
Binary expression of cell existence

Visualization

augment_genealogy() gggenealogy()
Visualize cell genealogy
plot_capture_rate()
Plot capture_rate ~ nsam of biopsy
plot_tumor3d() snapshot_surface() add_col()
3D plotting with rgl
histogram_freqspec() plot_lattice2d()
ggplot for frequency spectrum
save_serial_section()
Plot serial sections of 3D tumor

Read and Write

read_confs() read_results() read_populations() read_snapshots() read_tumopp()
Read TSV files in given directories
write_results()
Utilities for writing files