MIRA

DOI: 10.18129/B9.bioc.MIRA    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: 3.7

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MIRA")

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, MethylSeq, Sequencing, Software, SystemsBiology
Version	1.2.0
License	GPL-3
Depends	R (>= 3.4)
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
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MIRA_1.2.0.tar.gz
Windows Binary	MIRA_1.2.0.zip
Mac OS X 10.11 (El Capitan)	MIRA_1.2.0.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	http://bioconductor.org/packages/MIRA/
Package Downloads Report	Download Stats