DOI: 10.18129/B9.bioc.MIRA  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MIRA.

Methylation-Based Inference of Regulatory Activity

Bioconductor version: 3.16

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>

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


biocViews ChIPSeq, Coverage, DNAMethylation, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, ImmunoOncology, MethylSeq, Sequencing, Software, SystemsBiology
Version 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License GPL-3
Depends R (>= 3.5)
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods
Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
URL http://databio.org/mira
BugReports https://github.com/databio/MIRA
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Imports Me COCOA
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