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>

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

Installation

To install this package, start R (version "3.6") 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, ImmunoOncology, MethylSeq, Sequencing, Software, SystemsBiology
Version 1.6.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.5)
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
Imports Me COCOA
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/MIRA/
Package Short Url https://bioconductor.org/packages/MIRA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive