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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 forum

No open topic.

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

Documentation

Maintainer

Credits

Publications

Institution(s)

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

Link to literature

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