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MIRA

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 <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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MIRA")

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

Documentation

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

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

Details

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
System Requirements
URL http://databio.org/mira
Bug Reports https://github.com/databio/MIRA
See More
Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
Linking To
Enhances
Depends On Me
Imports Me COCOA
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MIRA_1.26.0.tar.gz
Windows Binary MIRA_1.26.0.zip
macOS Binary (x86_64) MIRA_1.26.0.tgz
macOS Binary (arm64) MIRA_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MIRA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MIRA
Bioc Package Browser https://code.bioconductor.org/browse/MIRA/
Package Short Url https://bioconductor.org/packages/MIRA/
Package Downloads Report Download Stats