ICBioMark {ICBioMark}

ICBioMark: A package for cost-effective design of gene panels to predict exome-wide biomarkers.

Description

This package implements the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', (Bradley and Cannings, 2021, preprint). It allows the user to fit generative models of mutation from an annotated mutation dataset, and then further to produce tunable linear estimators of exome-wide biomarkers. It also contains functions to simulate mutation annotated format (MAF) data, as well as to analyse the output and performance of models.