A method using maximum likelihood estimation to accurately estimate the parameters of unmethylated cytosine (5C), 5mC and 5hmC from Infinium microarray data given the signal intensities from the oxBS and BS replicates. The OxyBS tool can readily be applied to both the Illumina 450K and MethylationEPIC arrays as well as sequencing data with read counts for the four input data types (BS-methylated, BS-unmethylated, oxBSmethylated, and oxBS-unmethylated).

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OxyBS classification

OxyBS specifications

Software type:
Package
Restrictions to use:
None
Biological technology:
Illumina
Programming languages:
R
Version:
1.0
Requirements:
R (≥ 3.2.2)
Interface:
Command line interface
Output data:
The output is a user-friendly array containing estimates of 5C, 5mC, and 5hmC for each CpG on the array.
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Source code URL:
https://github.com/Christensen-Lab-Dartmouth/OxyBS

Publications

  • (Houseman et al., 2016) OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA. Bioinformatics.
    DOI: 10.1093/bioinformatics/btw158

OxyBS support

Documentation

Maintainer

Credits

Institution(s)

School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA; Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA

Funding source(s)

This work has been supported by the National Institutes of Health [grant numbers R01 MH094609, P20GM104416/8189].

Link to literature

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