Package: MIRA 1.34.0

John Lawson

MIRA: Methylation-Based Inference of Regulatory Activity

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.

Authors:Nathan Sheffield <http://www.databio.org> [aut], Christoph Bock [ctb], John Lawson [aut, cre]

MIRA_1.34.0.tar.gz
MIRA_1.34.0.zip(r-4.7)MIRA_1.34.0.zip(r-4.6)MIRA_1.34.0.zip(r-4.5)
MIRA_1.34.0.tgz(r-4.6-any)MIRA_1.34.0.tgz(r-4.5-any)
MIRA_1.34.0.tar.gz(r-4.7-any)MIRA_1.34.0.tar.gz(r-4.6-any)
MIRA_1.34.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MIRA/json (API)
NEWS

# Install 'MIRA' in R:
install.packages('MIRA', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/databio/mira/issues

Datasets:
  • bigBinDT1 - DNA methylation data for the "Applying MIRA to a Biological Question" vignette (1st part).
  • bigBinDT2 - DNA methylation data for the "Applying MIRA to a Biological Question" vignette (2nd part).
  • exampleAnnoDT1 - A data.table with annotation for a bisulfite sample.
  • exampleAnnoDT2 - Annotation data for the "Applying MIRA to a Biological Question" vignette.
  • exampleBins - A data.table with artificial binned methylation data
  • exampleBSDT - A data.table containing DNA methylation data.
  • exampleBSseqObj - A small BSseq object.
  • exampleRegionSet - A Granges object with Nrf1-binding regions.

On BioConductor:MIRA-1.35.0(bioc 3.24)MIRA-1.34.0(bioc 3.23)

immunooncologydnamethylationgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqmethylseqsequencingepigeneticscoverage

7.59 score 13 stars 1 packages 7 scripts 856 mentions 11 exports 87 dependencies

Last updated from:34b8921191 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE222
linux-devel-x86_64OK436
source / vignettesOK350
linux-release-x86_64OK452
macos-release-arm64OK221
macos-oldrel-arm64OK286
windows-develOK329
windows-releaseOK344
windows-oldrelOK363
wasm-releaseOK171

Exports:addMethPropColaggregateMethylbinRegionBSBinAggregateBSreadBiSeqbsseqToDataTablecalcMIRAScoreplotMIRAProfilesplotMIRAScoresrbindNamedListSummarizedExperimentToDataTable

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomebsseqcigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolsh5mreadHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml

Applying MIRA to a Biological Question

John Lawson

Rendered fromBiologicalApplication.Rmdusingknitr::rmarkdownon Jun 18 2026.

Last update: 2017-10-28
Started: 2017-04-25

Getting Started with Methylation-based Inference of Regulatory Activity

John Lawson

Rendered fromGettingStarted.Rmdusingknitr::rmarkdownon Jun 18 2026.

Last update: 2019-10-24
Started: 2017-04-25