MIRA

DOI: 10.18129/B9.bioc.MIRA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: 3.9

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>

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	1.6.0
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_1.6.0.tar.gz
Windows Binary	MIRA_1.6.0.zip
Mac OS X 10.11 (El Capitan)	MIRA_1.6.0.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