DOI: 10.18129/B9.bioc.MIRA    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: 3.8

MIRA measures the degree of "dip" in methylation level surrounding a regulatory site of interest, such as a transcription factor binding site, for instances of that type of site across the genome which can then be used to infer regulatory activity.

Author: Nathan Sheffield <http://www.databio.org> [aut], Christoph Bock [ctb], John Lawson [aut, cre]

Maintainer: John Lawson <jtl2hk at virginia.edu>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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:



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


biocViews ChIPSeq, Coverage, DNAMethylation, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, ImmunoOncology, MethylSeq, Sequencing, Software, SystemsBiology
Version 1.4.1
In Bioconductor since BioC 3.6 (R-3.4) (1.5 years)
License GPL-3
Depends R (>= 3.5)
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods
Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
URL http://databio.org/mira
BugReports https://github.com/databio/MIRA
Depends On Me
Imports Me COCOA
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package MIRA_1.4.1.tar.gz
Windows Binary MIRA_1.4.1.zip
Mac OS X 10.11 (El Capitan) MIRA_1.4.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/MIRA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MIRA
Package Short Url http://bioconductor.org/packages/MIRA/
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