HOME

HOME (Histogram Of MEthylation) is a software designed to accurately identify differentially methylated regions (DMRs) between samples in whole genome bisulfite sequencing data. It addresses the challenges existing DMR identification tools face, such as inaccurate boundary identification and high false positive rates.

HOME utilizes a unique approach based on the inherent differences in the distribution of methylation levels between DMRs and non-DMRs. It generates dataset-independent features and employs a Support Vector Machine to discriminate between DMRs and non-DMRs. It allows HOME to be trained on a specific dataset, such as a mouse methylome training set and then applied to datasets from any other organism to identify accurate DMRs.

Topic

Methylated DNA immunoprecipitation;Epigenetics;DNA

Detail

  • Operation: Whole genome methylation analysis;Gene methylation analysis;Bisulfite mapping

  • Software interface: Command-line interface

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: 1.0.0

  • Credit: The Australian Research Council (ARC) Centre of Excellence program in Plant Energy Biology, Sylvia and Charles Viertel Senior Medical Research Fellowship, ARC Future Fellowship, Howard Hughes Medical Institute International Research Scholarship.

  • Input: -

  • Output: -

  • Contact: Ryan Lister ryan.lister@uwa.edu.au

  • Collection: -

  • Maturity: Mature

Publications

  • HOME: a histogram based machine learning approach for effective identification of differentially methylated regions.
  • Srivastava A, et al. HOME: a histogram based machine learning approach for effective identification of differentially methylated regions. HOME: a histogram based machine learning approach for effective identification of differentially methylated regions. 2019; 20:253. doi: 10.1186/s12859-019-2845-y
  • https://doi.org/10.1186/S12859-019-2845-Y
  • PMID: 31096906
  • PMC: PMC6521357

Download and documentation

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