To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

MIRA

DOI: 10.18129/B9.bioc.MIRA    

Methylation-Based Inference of Regulatory Activity

Bioconductor version: Release (3.6)

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>

Citation (from within R, enter citation("MIRA")):

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

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 1.0.1
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
SystemRequirements
Enhances simpleCache
URL http://databio.org/mira
BugReports https://github.com/databio/MIRA
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package MIRA_1.0.1.tar.gz
Windows Binary MIRA_1.0.1.zip
Mac OS X 10.11 (El Capitan) MIRA_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/MIRA
Package Short Url http://bioconductor.org/packages/MIRA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

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