BIC_criterion           Bayesian Information Criterion
BIC_criterion_FLASH     Compute criterion FLASH
Cellular_preclustering
                        Preclustering method
CellularitiesFromFreq   Cellularities from allele frequency
Cluster_plot_from_cell
                        Cellularity clustering
Compute_NMI             Normalized Mutual Information
Compute_objective       Compute value of objective function
Create_prior_cutTree    Create priors from hierarchical clustering
EM.algo                 Expectation Maximization algorithm
EM_clustering           Expectation Maximization
FLASH_main              Flash core
FlashQC                 Flash QuantumClone
From_freq_to_cell       Wrap-up function
FullEM                  Expectation Maximization algorithm
Input_Example           Example generated by QuantumCat
MajorityVote            Majority vote
NMI_cutree              NMI
One_D_plot              Plots
One_step_clustering     Cellularity clustering
Patient_schrodinger_cellularities
                        Patient Schrodinger Cellularities
Precision_Recall        Precision
ProbDistMatrix          Distance
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
Tidy_output             Tidying output from EM
Tree                    Example of output by Tree_generation
Tree_generation         Phylogenetic tree
add_leaf_list           Phylogenetic tree leaf
check_leaf              Check created leaf
check_split             Check
create_priors           Clonal fraction prior creation
e.step                  Expectation step calculation
eval.fik.m              Eval probability for M step Computes the log
                        directly as log density is faster to compute
evolution_plot          Evolution plot
filter_on_fik           Data filter
find_x_position         Graphic position
grbase                  Computes gradient of function
grzero                  Gradient 0
hard.clustering         Hard clustering based on EM output
is_included             Group theory
list_prod               List product
longueur                Length
m.step                  Maximization step
manual_plot_trees       Plot tree
multiplot_trees         Plots multiple trees
parallelEM              Expectation Maximization algorithm
phylo_tree_generation   Data generation
plot_QC_out             Plot QC_output
plot_cell_from_Return_out
                        Plot cellularity
plot_with_margins_densities
                        Plot with margin densities
strcount                String count
update_probs            Update proportions
zscore                  Z-score
