×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

DMRcate

Online

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.

User report

×
Vote up tools and offer feedback
Give value to tools and make your expertise visible

0 user reviews

0 user reviews

No review has been posted.

DMRcate forum

×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.

No open topic.

DMRcate versioning

×
Upload and version your source code
Get your DOI for better tool traceability. Archive your releases so the community can easily visualize progress on you work.

No versioning.

DMRcate classification

DMRcate specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Version:
1.4.2
Requirements:
limma, minfi, DMRcatedata

DMRcate support

Documentation

Maintainer

  • Timothy J. Peters <>

Credits

×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.

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

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.