{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T02:30:58Z","timestamp":1772505058748,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,4,11]],"date-time":"2023-04-11T00:00:00Z","timestamp":1681171200000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>DNA methylation analysis using arrays is a widely used method in research and clinical studies to study Epigenetics. Although several packages have been published to incur the results, most of them require a deep computational knowledge to perform the analysis. To resolve the limitation and to offer an easily accessible solution for researchers, we developed methylR a graphical tool that can analyze not only the raw data but also performs different downstream analyses with a few mouse clicks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We used standard and established open-source published packages or pipelines in methylR. We evaluated a publicly available dataset and compared the published results with those obtained with our tool. We implemented eight downstream analysis modules that can perform multidimensional analyses to pathway enrichment. Although the main application is designed for Illumina DNA methylation array data analysis, we made the accessory modules suitable for other kinds of data analysis as well.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Freely available at Github: https:\/\/github.com\/JD2112\/methylr; Webserver: https:\/\/methylr.research.liu.se.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad184","type":"journal-article","created":{"date-parts":[[2023,4,11]],"date-time":"2023-04-11T15:05:58Z","timestamp":1681225558000},"source":"Crossref","is-referenced-by-count":6,"title":["methylR: a graphical interface for comprehensive DNA methylation array data analysis"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4184-5264","authenticated-orcid":false,"given":"Massimiliano","family":"Volpe","sequence":"first","affiliation":[{"name":"Bioinformatics Unit, Core Facility (KEF), Faculty of Medical and Health Sciences (BKV), Link\u00f6ping University , Link\u00f6ping SE-58185, Sweden"},{"name":"Clinical Genomics Link\u00f6ping, SciLife Laboratory, Department of Biomedical and Clinical Sciences, Link\u00f6ping University , Link\u00f6ping, SE-58185, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5649-4658","authenticated-orcid":false,"given":"Jyotirmoy","family":"Das","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Core Facility (KEF), Faculty of Medical and Health Sciences (BKV), Link\u00f6ping University , Link\u00f6ping SE-58185, Sweden"},{"name":"Clinical Genomics Link\u00f6ping, SciLife Laboratory, Department of Biomedical and Clinical Sciences, Link\u00f6ping University , Link\u00f6ping, SE-58185, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2023,4,11]]},"reference":[{"key":"2023042502095817800_btad184-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":"2023042502095817800_btad184-B2","author":"Chang","year":"2023"},{"key":"2023042502095817800_btad184-B3","doi-asserted-by":"crossref","DOI":"10.1080\/15592294.2021.1969499","article-title":"DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell 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