MIRA

DOI: 10.18129/B9.bioc.MIRA    

This is the development version of MIRA; for the stable release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: Development (3.8)

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:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("MIRA", version = "devel")

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 1.3.0
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
Build Report  

Package Archives

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

Source Package MIRA_1.3.0.tar.gz
Windows Binary MIRA_1.3.0.zip
Mac OS X 10.11 (El Capitan) MIRA_1.3.0.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

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