{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T07:58:01Z","timestamp":1776326281843,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,1,8]],"date-time":"2021-01-08T00:00:00Z","timestamp":1610064000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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. shiny\u00c9PICo is an interactive, web-based, and graphical tool that allows the user to analyze Illumina DNA methylation arrays (450k and EPIC), from the user\u2019s 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. shiny\u00c9PICo represents a comprehensive tool for standardizing and accelerating DNA methylation analysis, as well as optimizing computational resources in laboratories studying DNA methylation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>shiny\u00c9PICo 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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1095","type":"journal-article","created":{"date-parts":[[2020,12,23]],"date-time":"2020-12-23T04:24:37Z","timestamp":1608697477000},"page":"257-259","source":"Crossref","is-referenced-by-count":26,"title":["shiny\u00c9PICo: a graphical pipeline to analyze Illumina DNA methylation arrays"],"prefix":"10.1093","volume":"37","author":[{"given":"Octavio","family":"Morante-Palacios","sequence":"first","affiliation":[{"name":"Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC) , 08916 Badalona, Spain"},{"name":"Germans Trias i Pujol Research Institute (IGTP) , 08916 Badalona, Spain"}]},{"given":"Esteban","family":"Ballestar","sequence":"additional","affiliation":[{"name":"Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC) , 08916 Badalona, Spain"},{"name":"Germans Trias i Pujol Research Institute (IGTP) , 08916 Badalona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2021,1,8]]},"reference":[{"key":"2023051510472517100_btaa1095-B1","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1093\/bioinformatics\/btu049","article-title":"Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays","volume":"30","author":"Aryee","year":"2014","journal-title":"Bioinformatics"},{"key":"2023051510472517100_btaa1095-B2","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1038\/s41591-018-0028-4","article-title":"The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia","volume":"24","author":"Beekman","year":"2018","journal-title":"Nat. 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