MIRA: an R package for DNA methylation-based inference of regulatory activity

John T Lawson; Eleni M Tomazou; Christoph Bock; Nathan C Sheffield

doi:10.1093/bioinformatics/bty083

MIRA: an R package for DNA methylation-based inference of regulatory activity

Bioinformatics. 2018 Aug 1;34(15):2649-2650. doi: 10.1093/bioinformatics/bty083.

Authors

John T Lawson^{1

2}, Eleni M Tomazou³, Christoph Bock⁴, Nathan C Sheffield²

Affiliations

¹ Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
² Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
³ Children's Cancer Research Institute, St. Anna's Kinderkrebsforschung, Vienna, Austria.
⁴ CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

Abstract

Summary: DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.

Availability and implementation: http://bioconductor.org/packages/MIRA.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Biological Ontologies
Computational Biology / methods
DNA Methylation*
Epigenomics / methods*
Sequence Analysis, DNA / methods*
Software*

Abstract

Publication types

MeSH terms

Grants and funding