Aneuvis: Web-based exploration of numerical chromosomal variation in single cells

Abstract

MotivationAberrations in chromosomal copy number are one of the most common molecular features observed in cancer. Quantifying the degree of numerical chromosomal variation in single cells across a population of cells is of interest to researchers studying whole chromosomal instability (W-CIN). W-CIN, a state of high numerical chromosomal variation, contributes to treatment resistance in cancer.\n\nResultsHere, we introduce aneuvis, a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation.\n\nAvailability and ImplementationAneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/. Website implemented using Shiny version 1.0.5 with all major browsers supported. All source code for the application is available at https://github.com/dpique/aneuvis.