Package: MIRA 1.29.0

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_1.29.0.tar.gz
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MIRA.pdf |MIRA.html✨
MIRA/json (API)
NEWS

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

Peer review:

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.
  • exampleBSDT - A data.table containing DNA methylation data.
  • exampleBSseqObj - A small BSseq object.
  • exampleBins - A data.table with artificial binned methylation data
  • exampleRegionSet - A Granges object with Nrf1-binding regions.

On BioConductor:MIRA-1.27.0(bioc 3.20)MIRA-1.26.0(bioc 3.19)

immunooncologydnamethylationgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqmethylseqsequencingepigeneticscoverage

7.52 score 11 stars 1 packages 7 scripts 208 downloads 856 mentions 11 exports 94 dependencies

Last updated 21 days agofrom:699390ad86. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:addMethPropColaggregateMethylbinRegionBSBinAggregateBSreadBiSeqbsseqToDataTablecalcMIRAScoreplotMIRAProfilesplotMIRAScoresrbindNamedListSummarizedExperimentToDataTable

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebsseqclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsfansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolsHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpermutepillarpkgconfigR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

Applying MIRA to a Biological Question

John Lawson

Rendered fromBiologicalApplication.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Getting Started with Methylation-based Inference of Regulatory Activity

John Lawson

Rendered fromGettingStarted.Rmdusingknitr::rmarkdownon Oct 30 2024.

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