Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing
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 I...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2016-10-01
|
| Series: | Journal of Integrative Bioinformatics |
| Online Access: | https://doi.org/10.1515/jib-2016-294 |
| _version_ | 1818733572943511552 |
|---|---|
| author | Almeida Diogo Skov Ida Lund Jesper Mohammadnejad Afsaneh Silva Artur Vandin Fabio Tan Qihua Baumbach Jan Röttger Richard |
| author_facet | Almeida Diogo Skov Ida Lund Jesper Mohammadnejad Afsaneh Silva Artur Vandin Fabio Tan Qihua Baumbach Jan Röttger Richard |
| author_sort | Almeida Diogo |
| collection | DOAJ |
| description | 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 |
| first_indexed | 2024-12-17T23:51:36Z |
| format | Article |
| id | doaj.art-099aef4d079141dda40083ac85e19752 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-17T23:51:36Z |
| publishDate | 2016-10-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-099aef4d079141dda40083ac85e197522022-12-21T21:28:11ZengDe GruyterJournal of Integrative Bioinformatics1613-45162016-10-01134243210.1515/jib-2016-294jib-2016-294Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processingAlmeida Diogo0Skov Ida1Lund Jesper2Mohammadnejad Afsaneh3Silva Artur4Vandin Fabio5Tan Qihua6Baumbach Jan7Röttger Richard8Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230Odense, DenmarkDepartment of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230Odense, DenmarkDepartment of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230Odense, DenmarkDepartment of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230Odense, DenmarkLaboratory for Genomics and Bioinformatic, Institute of Biological Sciences, Federal University of Pará, 66075110, Belém, BrazilDepartament of Information Engineering, University of Padova, Via Gradenigo 6/B, I-35131Padova, ItalyUnit of Human Genetics, Department of Clinical Research, Faculty of Health Science, University of Southern Denmark, 5000Odense, DenmarkDepartment of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230Odense, DenmarkDepartment of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230Odense, DenmarkMeasuring 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.htmlhttps://doi.org/10.1515/jib-2016-294 |
| spellingShingle | Almeida Diogo Skov Ida Lund Jesper Mohammadnejad Afsaneh Silva Artur Vandin Fabio Tan Qihua Baumbach Jan Röttger Richard Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing Journal of Integrative Bioinformatics |
| title | Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing |
| title_full | Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing |
| title_fullStr | Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing |
| title_full_unstemmed | Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing |
| title_short | Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing |
| title_sort | jllumina a comprehensive java based api for statistical illumina infinium humanmethylation450 and infinium methylationepic beadchip data processing |
| url | https://doi.org/10.1515/jib-2016-294 |
| work_keys_str_mv | AT almeidadiogo jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT skovida jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT lundjesper jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT mohammadnejadafsaneh jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT silvaartur jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT vandinfabio jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT tanqihua jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT baumbachjan jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing AT rottgerrichard jlluminaacomprehensivejavabasedapiforstatisticalilluminainfiniumhumanmethylation450andinfiniummethylationepicbeadchipdataprocessing |