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A package that fits replicated methylation measurements from the Illumina HM450K BeadChip (or 450K array) spatially across the genome using a Gaussian kernel. DMRcate identifies and ranks the most differentially methylated regions across the genome based on tunable kernel smoothing of the differential methylation (DM) signal. The method is agnostic to both genomic annotation and local change in the direction of the DM signal, removes the bias incurred from irregularly spaced methylation sites, and assigns significance to each DMR called via comparison to a null model. DMRcate provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. It includes bedGraph generation, GRanges generation and plotting functions.

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DMRcate versioning

No versioning.

DMRcate classification

DMRcate specifications

Software type:
Package
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Version:
DMRcate version 1.4.2
Requirements:
R (>= 3.1.3), limma, minfi, DMRcatedata

DMRcate support

Maintainer

Credits

Publications

  • (Peters et al., 2015) De novo identification of differentially methylated regions in the human genome. Epigenetics & chromatin.
    PMID: 25972926

Institution(s)

CSIRO Digital Productivity Flagship, Riverside Life Sciences Centre, 11 Julius Avenue, North Ryde, New South Wales 2113, Australia; Epigenetics Program, Garvan Institute of Medical Research, Sydney, Australia; St Vincent’s Hospital, Darlinghurst, New South Wales 2010, Australia; School of Medicine, University of Notre Dame, Darlinghurst, New South Wales 2010, Australia; St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia; CSIRO Food and Nutrition Flagship, Riverside Life Sciences Centre, 11 Julius Avenue, Sydney, Australia

Link to literature

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