CMUSchwartzLab

cancer-phylogenetics-prognostic-prediction

Improving Personalized Prediction of Cancer Prognoses with Clonal Evolution Models

TUSV-ext

RAD

Robust and Accurate Deconvolution

RADs

FISH_deconvolution

code implementing methods for pooling bulk and single cell data and FISH data for copy number deconvolution

NND

Neural network deconvolution

ConTreeDP

Consensus method for tumor history tree based on directed partitions using dynamic programming

JointClustering

The joint clustering method for single cell miFISH and single cell whole genome copy numbers

MosaicSim

SCS_deconvolution

code implementing methods for pooling bulk and single cell data for copy number deconvolution

BrM-Phylo

Phylogenies of Breast Cancer Brain Metastases

Sc-TUSV-ext

Sc-TUSV-ext: Tumor evolutionary tree reconstruction from single-cell DNA-seq data of single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV).

SimGenome

Simulation of the somatic variations (structural variations, copy number variations and single nucleotide variations) in whole genome based on tumor phylogenetic trees. SimGenome is the simulation method used in TUSV-ext project.

Mase-phi

Marker selection strategies for ctDNA guided by phylogenetic inference

StudyDesignOptimization