We have developed several software tools for analysis of genetic alterations that occur in cancer.
Mutation Enrichment Gene set Analysis of Variants (MEGA-V) is an open-source R application with a Shiny web interface. It identifies gene sets with a significantly higher number of variants in a cohort of interest (cohort A) as compared to (1) a control cohort (cohort B) or (2) a random distribution generated using Monte Carlo.
Network of Cancer Genes (NCG) is a publicly available manually curated repository of cancer genes and associated properties from cancer mutational screenings.
sysSVM is an algorithm to identify genes that are similar to known cancer genes according to system-level properties of the gene and type/number of alterations in tumours of cancer samples. The algorithm uses machine learning, specifically it uses four support vector machines (SVMs) with four different kernel functions (linear, polynomial, radial, and sigmoid).