Interactive DNA Methylation Array Analysis with ShinyÉPICo

Octavio Morante-Palacios

doi:10.1007/978-1-0716-2962-8_2

Interactive DNA Methylation Array Analysis with ShinyÉPICo

Methods Mol Biol. 2023:2624:7-18. doi: 10.1007/978-1-0716-2962-8_2.

Author

Octavio Morante-Palacios^{1

2}

Affiliations

¹ Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain.
² Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain.

PMID: 36723806
DOI: 10.1007/978-1-0716-2962-8_2

Abstract

Arrays provide a cost-effective platform for the analysis of human DNA methylation. ShinyÉPICo is an interactive, web-based, and graphical tool that allows the user to analyze Illumina DNA methylation arrays (450 k and EPIC), from the user's own computer or from a server. This tool covers the analysis entirely, from the raw data input to the final list of differentially methylated positions or regions. Here, we describe the steps of the analysis, the different parameters available, and useful information to understand and select the best options in each step.

Keywords: DNA methylation; Differentially Methylated Positions; Differentially Methylated Regions; Epigenetics; Shiny; Web Interface.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CpG Islands
DNA Methylation*
Data Interpretation, Statistical
Humans
Software*