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Methylation-Based Inference of Regulatory Activity

Bioconductor version: Release (3.19)

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.

Author: Nathan Sheffield <> [aut], Christoph Bock [ctb], John Lawson [aut, cre]

Maintainer: John Lawson <jtl2hk at>

Citation (from within R, enter citation("MIRA")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Applying MIRA to a Biological Question HTML R Script
Getting Started with Methylation-based Inference of Regulatory Activity HTML R Script
Reference Manual PDF


biocViews ChIPSeq, Coverage, DNAMethylation, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, ImmunoOncology, MethylSeq, Sequencing, Software, SystemsBiology
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.5)
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods
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Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
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Follow Installation instructions to use this package in your R session.

Source Package MIRA_1.26.0.tar.gz
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macOS Binary (x86_64) MIRA_1.26.0.tgz
macOS Binary (arm64) MIRA_1.26.0.tgz
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