| add_leaf_list | Phylogenetic tree leaf |
| BIC_criterion | Bayesian Information Criterion |
| CellularitiesFromFreq | Cellularities from allele frequency |
| Cluster_plot_from_cell | Cellularity clustering |
| create_priors | Clonal fraction prior creation |
| e.step | Expectation step calculation |
| EM.algo | Expectation Maximization algorithm |
| EM_clustering | Expectation Maximization |
| evolution_plot | Evolution plot |
| filter_on_fik | Data filter |
| find_x_position | Graphic position |
| From_freq_to_cell | Wrap-up function |
| FullEM | Expectation Maximization algorithm |
| hard.clustering | Hard clustering based on EM output |
| Input_Example | Example generated by QuantumCat |
| is_included | Group theory |
| list_prod | List product |
| longueur | Length |
| m.step | Maximization step |
| manual_plot_trees | Plot tree |
| multiplot_trees | Plots multiple trees |
| Multitest | Multiple testing |
| One_D_plot | Plots |
| One_step_clustering | Cellularity clustering |
| parallelEM | Expectation Maximization algorithm |
| Patient_schrodinger_cellularities | Patient Schrodinger Cellularities |
| phylo_tree_generation | Data generation |
| plot_cell_from_Return_out | Plot cellularity |
| plot_QC_out | Plot QC_output |
| plot_with_margins_densities | Plot with margin densities |
| Probability.to.belong.to.clone | Probability |
| QC_output | Example of output generated by clustering of Input_Example |
| QuantumCat | Data generation |
| QuantumClone | One step analysis function |
| statistics_on_Multitest | Multiple testing |
| strcount | String count |
| ThreeD_plot | 3D Plot |
| Tree | Example of output by Tree_generation |
| Tree_generation | Phylogenetic tree |