MIRA

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: 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 (!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

Need some help? Ask on the Bioconductor Support site!

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) (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

Suggests	knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
Linking To
Enhances
Depends On Me
Imports Me	COCOA
Suggests Me
Links To Me
Build Report	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
Bioc Package Browser	https://code.bioconductor.org/browse/MIRA/
Package Short Url	https://bioconductor.org/packages/MIRA/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.10	Source Archive