LACHESIS                Run MRCA density estimation for a set of tumors
MRCA                    Compute mutation densities at ECA and MRCA
classifyLACHESIS        Classify a tumor's start of clonal outgrowth
                        during tumorigenesis as "Early MRCA" or "Late
                        MRCA" (favorable/ unfavorable prognosis)
                        depending on the mutation density at its MRCA
clonalMutationCounter   Count clonal mutations on one or several
                        chromosomal copies
estimateClonality       Assigning clonality status to every SNV
nbImport                Combine CNVs and SNVs
normalizeCounts         Normalize clonal mutation counts
plotClinicalCorrelations
                        Correlate SNV density at ECA/MRCA with clinical
                        parameters such as age, OS, etc.
plotClonality           Plotting assigned clonality status for every
                        SNV by chromosome
plotDiseaseTrajectories
                        Plot the disease trajectories in a cohort.
plotLachesis            Plot SNV densities at ECA and MRCA
plotMutationDensities   Plot normalized mutation density at copy number
                        gain and MRCA per segment
plotNB                  Plot VAF distribution per copy number
plotSurvival            Correlate SNV density timing at MRCA with
                        Survival
plotVAFdistr            Plot histogram of VAF distribution
readCNV                 Converts a user-specified bed-file with copy
                        number information into a standardized format
                        that can be used as input for downstream
                        analysis
readVCF                 Import a VCF file and extract read count
