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Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing

Almeida, Diogo ; Skov, Ida ; Lund, Jesper ; Mohammadnejad, Afsaneh ; Silva, Artur ; Vandin, Fabio ; Tan, Qihua ; Baumbach, Jan ; Röttger, Richard

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Almeida, Diogo ; Skov, Ida ; Lund, Jesper ; Mohammadnejad, Afsaneh ; Silva, Artur ; Vandin, Fabio ; Tan, Qihua ; Baumbach, Jan ; Röttger, Richard  (2016)  Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 13(4): Special Issue: 12th International Symposium on Integrative Bioinformatics, Bielefeld, Germany, 2016

Online-Journal: http://journal.imbio.de/article.php?aid=294
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2017/5434



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