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>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("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")
Applying MIRA to a Biological Question HTML R Script
Getting Started with Methylation-based Inference of Regulatory Activity HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Coverage, DNAMethylation, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, MethylSeq, Sequencing, Software, SystemsBiology
Version 1.2.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.4)
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods
System Requirements
URL http://databio.org/mira
Bug Reports https://github.com/databio/MIRA
See More
Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
Linking To
Enhances
Depends On Me
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Build Report 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 https://bioconductor.org/packages/MIRA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive