shinyÉPICo: a graphical pipeline to analyze Illumina DNA methylation arrays
Octavio Morante-Palacios, Esteban Ballestar
Abstract
SUMMARY: Illumina DNA methylation bead arrays provide a cost-effective platform for the simultaneous analysis of a high number of human samples. However, the analysis can be time-demanding and requires some computational expertise. shinyÉPICo is an interactive, web-based, and graphical tool that allows the user to analyze Illumina DNA methylation arrays (450k and EPIC), from the user's own computer or from a server. The tool covers the entire analysis, from the raw data to the final list of differentially methylated positions and differentially methylated regions between sample groups. It allows the user to test several normalization methods, linear model parameters, including covariates, and differentially methylated CpGs filters, in a quick and easy manner, with interactive graphics helping to select the options in each step. shinyÉPICo represents a comprehensive tool for standardizing and accelerating DNA methylation analysis, as well as optimizing computational resources in laboratories studying DNA methylation. AVAILABILITY AND IMPLEMENTATION: shinyÉPICo is freely available as an R package at the Bioconductor project (http://bioconductor.org/packages/shinyepico/) and GitHub (https://github.com/omorante/shinyepico) under an AGPL3 license.