MIRA

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: 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 (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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, Coverage, DNAMethylation, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, ImmunoOncology, MethylSeq, Sequencing, Software, SystemsBiology

Version 1.4.1

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

Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA

Linking To

Enhances

Depends On Me

Imports Me COCOA

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Build Report Build Report

Package Archives

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

Source Package MIRA_1.4.1.tar.gz

Windows Binary MIRA_1.4.1.zip

Mac OS X 10.11 (El Capitan) MIRA_1.4.1.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 3.8 Source Archive