MIRA

DOI: 10.18129/B9.bioc.MIRA    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") 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	1.14.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 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_1.14.0.tar.gz
Windows Binary	MIRA_1.14.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	MIRA_1.14.0.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