Morante-Palacios Octavio, Ballestar Esteban
Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Spain.
Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain.
Bioinformatics. 2021 Apr 19;37(2):257-259. doi: 10.1093/bioinformatics/btaa1095.
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.
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.
Illumina DNA甲基化微珠芯片为同时分析大量人类样本提供了一个经济高效的平台。然而，该分析可能耗时且需要一些计算专业知识。shinyÉPICo是一个交互式的、基于网络的图形工具，允许用户从自己的计算机或服务器上分析Illumina DNA甲基化芯片（450k和EPIC）。该工具涵盖了从原始数据到样本组之间差异甲基化位点和差异甲基化区域的最终列表的整个分析过程。它允许用户以快速简便的方式测试多种标准化方法、线性模型参数（包括协变量）和差异甲基化CpG过滤器，交互式图形有助于在每个步骤中选择选项。shinyÉPICo是一个用于标准化和加速DNA甲基化分析以及优化研究DNA甲基化的实验室中的计算资源的综合工具。
shinyÉPICo作为一个R包，在AGPL3许可下可在Bioconductor项目（http://bioconductor.org/packages/shinyepico/）和GitHub（https://github.com/omorante/shinyepico）上免费获取。
