ipDMR

ipDMR is an R software tool designed to identify differentially methylated regions (DMRs) by leveraging auto-correlated P-values from individual CpGs obtained through epigenome-wide association analysis using array or bisulfite sequencing data. The tool aggregates P-values for adjacent CpGs, locates association peaks, and extends these peaks to define DMR boundaries. Utilizing BED format files as input, ipDMR is user-friendly.

Topic

Epigenetics;Microarray experiment;Methylated DNA immunoprecipitation;DNA

Detail

  • Operation: DMR identification;Gene methylation analysis;Regression analysis;Validation

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.38.01

  • Credit: The Intramural Research Program of the NIH, National Institute of Environmental Health Sciences, National Institute of Environmental Health Sciences.

  • Input: BED

  • Output: -

  • Contact: Zongli Xu xuz@niehs.nih.gov

  • Collection: -

  • Maturity: Stable

Publications

  • ipDMR: identification of differentially methylated regions with interval P-values.
  • Xu Z, et al. ipDMR: identification of differentially methylated regions with interval P-values. ipDMR: identification of differentially methylated regions with interval P-values. 2021; 37:711-713. doi: 10.1093/bioinformatics/btaa732
  • https://doi.org/10.1093/BIOINFORMATICS/BTAA732
  • PMID: 32805005
  • PMC: PMC8248314

Download and documentation

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