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("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 | ||
| 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 |