zanmer / mesothelioma_evolution_deciphering_drugable_somatic_alterations

Analysis scripts and relative data used in the paper "Clonal Architecture in Mesothelioma is prognostic and shapes the Tumour Microenvironment" by Zhang et al.

Mesothelioma_evolution_deciphering_drugable_somatic_alterations

Analysis scripts and relative data used in the paper "Clonal Architecture in Mesothelioma is prognostic and shapes the Tumour Microenvironment" by Zhang et al.

data

contains many .Rdata files ready to use in the analysis.

code

clonal_analysis.R: This script is used to calculate cancer cell fraction of somatic mutations, and generate input TSV files for PyClone clusterings analysis.

dndscv_analysis.R: This script is used to run dndsCV analysis both for clonal and subclonal mutations.

mutational_signature_analysis.R: This script is used to deconstruct mutational signature contributions based on COSMICV3 reference.

revolver_analysis.R: This script is used to perform REVOLVER analysis to construct phylogeny trees and infer repeat evolution trajectories in MEDUSA22 cohort.