A method to map DNA methylation data from bisulfite sequencing approaches to CpG sites measured with the widely used Illumina methylation bead-array platforms. Correlations and median absolute deviations support the validity of using bisulfite sequencing data in combination with Illumina bead-array methylation data. The methyLiftover utility will enhance the field of epigenomic research by expanding the comparability of DNA methylation data in the absence of the common Illumina 450K methylation data. The methyLiftover tool contains functions to subset and map WGBS and RRBS data to the CpG sites specific to the Illumina 450K array, both individually and as a whole directory, and create merged data sets from two user defined methylation data files (e.g. Illumina 850K annotation).

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2 user reviews

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Kevin C. Johnson

Easy to use and detailed documentation. Maintainer responded promptly to inquiries.

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David Chen

methyLiftover operates on multiple types of genome-scale DNA methylation data and works compatibly with other R/Bioconductor packages. Highly recommend!

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methyLiftover classification

methyLiftover specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
R
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced

methyLiftover support

Maintainer

Credits

Publications

Institution(s)

Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA; Department of Biostatistics, Oregon State University College of Public Health and Human Sciences, Corvallis, OR, USA; Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA; Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA

Funding source(s)

This work has been supported by P20GM104416/8189 (BCC), R01DE022772 (BCC), R01MH094609 (EAH) and R01ES024991 (EAH).

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