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methylR: a graphical interface for comprehensive DNA methylation array data analysis
Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.ORCID iD: 0000-0003-4184-5264
Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.ORCID iD: 0000-0002-5649-4658
2023 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 39, no 4, article id btad184Article in journal (Refereed) Published
Abstract [en]

Motivation: 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.Results: 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.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2023. Vol. 39, no 4, article id btad184
National Category
Computer Sciences
Identifiers
URN: urn:nbn:se:liu:diva-194189DOI: 10.1093/bioinformatics/btad184ISI: 000978639900002PubMedID: 37039839OAI: oai:DiVA.org:liu-194189DiVA, id: diva2:1760970
Note

Funding Agencies|Linkoeping University IT Department

Available from: 2023-05-31 Created: 2023-05-31 Last updated: 2023-12-27

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