{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T18:44:42Z","timestamp":1759776282513},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T00:00:00Z","timestamp":1479081600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Epigenome-wide association studies (EWAS) generate big epidemiological datasets. They aim for detecting differentially methylated DNA regions that are likely to influence transcriptional gene activity and, thus, the regulation of metabolic processes. The by far most widely used technology is the Illumina Methylation BeadChip, which measures the methylation levels of 450 (850) thousand cytosines, in the CpG dinucleotide context in a set of patients compared to a control group. Many bioinformatics tools exist for raw data analysis. However, most of them require some knowledge in the programming language R, have no user interface, and do not offer all necessary steps to guide users from raw data all the way down to statistically significant differentially methylated regions (DMRs) and the associated genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we present DiMmeR (Discovery of Multiple Differentially Methylated Regions), the first free standalone software that interactively guides with a user-friendly graphical user interface (GUI) scientists the whole way through EWAS data analysis. It offers parallelized statistical methods for efficiently identifying DMRs in both Illumina 450K and 850K EPIC chip data. DiMmeR computes empirical P-values through randomization tests, even for big datasets of hundreds of patients and thousands of permutations within a few minutes on a standard desktop PC. It is independent of any third-party libraries, computes regression coefficients, P-values and empirical P-values, and it corrects for multiple testing.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>DiMmeR is publicly available at http:\/\/dimmer.compbio.sdu.dk.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw657","type":"journal-article","created":{"date-parts":[[2016,10,13]],"date-time":"2016-10-13T11:06:38Z","timestamp":1476356798000},"page":"549-551","source":"Crossref","is-referenced-by-count":7,"title":["Efficient detection of differentially methylated regions using DiMmeR"],"prefix":"10.1093","volume":"33","author":[{"given":"Diogo","family":"Almeida","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark"},{"name":"Laboratory for Genomics and Bioinformatics, Institute of Biological Sciences, Federal University of Par\u00e1, Bel\u00e9m, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ida","family":"Skov","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Artur","family":"Silva","sequence":"additional","affiliation":[{"name":"Laboratory for Genomics and Bioinformatics, Institute of Biological Sciences, Federal University of Par\u00e1, Bel\u00e9m, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabio","family":"Vandin","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark"},{"name":"Department of Information Engineering, University of Padova, Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qihua","family":"Tan","sequence":"additional","affiliation":[{"name":"Clinical Institute (CI), University of Southern Denmark, Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"R\u00f6ttger","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Baumbach","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark"},{"name":"Max Planck Institute for Informatics, Saarbruecken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,11,14]]},"reference":[{"key":"2023020204422898300_btw657-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":"2023020204422898300_btw657-B2","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1038\/nmeth.3115","article-title":"Comprehensive analysis of dna methylation data with rnbeads","volume":"11","author":"Assenov","year":"2014","journal-title":"Nat. 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