The Ciccarelli group has developed a number of tools and software for use with computational biology pipelines:
MEGA-V (Mutation Enrichment Gene set Analysis of Variants) is an open-source R application to identify over-represented pathways of variant genes across cohorts to map mutation information to perturbed biological processes.
Network of Cancer Genes (NCG) is a publicly available and manually curated repository of cancer and healthy drivers from cancer and healthy tissue mutational screens.
sysSVM is an open-source algorithm to identify cancer driver genes at patient resolution using machine learning.
SIMPLI (Single-cell Identification from MultiPLexed Images) is an end-to-end software for the analysis of high-dimensional tissue images. It is flexible and technology-agnostic and unifies all steps of multiplexed imaging data analysis.