Package: MIRA 1.35.0

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_1.35.0.tar.gz
MIRA_1.35.0.zip(r-4.7)MIRA_1.35.0.zip(r-4.6)MIRA_1.35.0.zip(r-4.5)
MIRA_1.35.0.tgz(r-4.6-any)MIRA_1.35.0.tgz(r-4.5-any)
MIRA_1.35.0.tar.gz(r-4.7-any)MIRA_1.35.0.tar.gz(r-4.6-any)
MIRA_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MIRA/json (API)

# Install 'MIRA' in R:
install.packages('MIRA', repos = c('https://bioc.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 88 dependencies

Last updated from:bd35b236f8. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE219
linux-devel-x86_64OK469
source / vignettesOK387
linux-release-x86_64OK468
macos-release-arm64OK261
macos-oldrel-arm64OK217
windows-develOK348
windows-releaseOK313
windows-oldrelOK326
wasm-releaseOK221

Exports:addMethPropColaggregateMethylbinRegionBSBinAggregateBSreadBiSeqbsseqToDataTablecalcMIRAScoreplotMIRAProfilesplotMIRAScoresrbindNamedListSummarizedExperimentToDataTable

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomebsseqcigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolsh5mreadHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml

Getting Started with Methylation-based Inference of Regulatory Activity
The MIRA Bioconductor package | Required inputs | DNA methylation data | Region sets | Analysis workflow | The input | Expand your regions | Aggregating methylation across regions | Calculating the MIRA score | Interpreting the results | Bonus: Loading region sets with LOLA
Rendered fromGettingStarted.Rmdusingknitr::rmarkdown

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

Applying MIRA to a Biological Question
Biological Question | Input: | Package workflow | Initial Run-through | Choosing Appropriate Region Sizes | Full MIRA Analysis | Interpreting the Results | General Interpretation Tips and Caveats | Other Tips for Using MIRA
Rendered fromBiologicalApplication.Rmdusingknitr::rmarkdown

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