MIRA
This is the development version of MIRA; for the stable release version, see MIRA.
Methylation-Based Inference of Regulatory Activity
Bioconductor version: Development (3.21)
DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.29.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | MIRA_1.29.0.zip |
| macOS Binary (x86_64) | MIRA_1.29.0.tgz |
| macOS Binary (arm64) | |
| 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 |