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An efficient method based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that oxBS-MLE outperformed alternative methods in estimate accuracy and computation speed.

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oxBS-MLE classification

oxBS-MLE specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Requirements:
minfi, parallel, doParallel, Biobase, foreach
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Stability:
Stable

oxBS-MLE support

Maintainer

Additional information

oxBS-MLE is implemented in Bioconductor package ENmix.

Credits

Publications

  • (Xu et al., 2016) oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics.
    PMID: 27522082

Institution(s)

Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA

Funding source(s)

This research was supported by the Center for Environmental Genetics grant (NIEHS award P30ES00606), NIEHS grant ES022071, and Intramural Research Program of the NIH (NIEHS Z01 ES049033, and Z01 ES049032).

Link to literature

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