MMRD classification using indels at microsatellites and signatures jo…

…intly

functions to add indels features to input data table, and simulation/…

…training jointly with Sig3 to classify HRD, currently limited built-in simulation matrices

functionalities to extract more information about WGS cluster centroi…

…ds that are matched to data

more flexible training for detection of signatures other than Sig3

MMRD classifiers using MMRD-specific signatures and indels at microsa…

…tellites

new functions for users to generate quick simulations, train classifi…

…ers and adjust thresholds on Sig3 score to obtain specific FPR

contains Sig3 classifiers, TCGA-MC3 calls are used to generate simula…

…tions from WGS

matches mutations in a panel/WES or WGS with a likelihood measure to …

…WGS clusers in tumor type specific way, plus, contains Sig3 classifiers using gradient boosting trees for MSK-IMPACT panels, WES data WGS data