MIRA

DOI: 10.18129/B9.bioc.MIRA    

Methylation-Based Inference of Regulatory Activity

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews ChIPSeq, Coverage, DNAMethylation, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, ImmunoOncology, MethylSeq, Sequencing, Software, SystemsBiology
Version 1.8.0
In Bioconductor since BioC 3.6 (R-3.4) (2 years)
License GPL-3
Depends R (>= 3.5)
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods
LinkingTo
Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
SystemRequirements
Enhances
URL http://databio.org/mira
BugReports https://github.com/databio/MIRA
Depends On Me
Imports Me COCOA
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MIRA_1.8.0.tar.gz
Windows Binary MIRA_1.8.0.zip
Mac OS X 10.11 (El Capitan) MIRA_1.8.0.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 https://bioconductor.org/packages/MIRA/
Package Downloads Report Download Stats

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