Package: DMRcaller 1.44.0

Nicolae Radu Zabet

DMRcaller: Differentially Methylated Regions Caller

Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.

Authors:Nicolae Radu Zabet <[email protected]>, Jonathan Michael Foonlan Tsang <[email protected]>, Alessandro Pio Greco <[email protected]>, Ryan Merritt <[email protected]> and Young Jun Kim <[email protected]>

DMRcaller_1.44.0.tar.gz
DMRcaller_1.44.0.zip(r-4.7)DMRcaller_1.44.0.zip(r-4.6)DMRcaller_1.44.0.zip(r-4.5)
DMRcaller_1.44.0.tgz(r-4.6-any)DMRcaller_1.44.0.tgz(r-4.5-any)
DMRcaller_1.44.0.tar.gz(r-4.7-any)DMRcaller_1.44.0.tar.gz(r-4.6-any)
DMRcaller_1.44.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DMRcaller/json (API)
NEWS

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

On BioConductor:DMRcaller-1.45.0(bioc 3.24)DMRcaller-1.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

differentialmethylationdnamethylationsoftwaresequencingcoverage

5.63 score 64 scripts 444 downloads 6 mentions 33 exports 72 dependencies

Last updated from:a828fa4003 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

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bioc-checksNOTE272
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source / vignettesOK396
linux-release-x86_64NOTE676
macos-release-arm64NOTE555
macos-oldrel-arm64NOTE433
windows-develNOTE581
windows-releaseNOTE619
windows-oldrelNOTE637
wasm-releaseOK229

Exports:analyseReadsInsideRegionsForConditionanalyseReadsInsideRegionsForConditionPMDcomputeCoMethylatedPositionscomputeCoMethylatedRegionscomputeDMRscomputeDMRsReplicatescomputeMethylationDataCoveragecomputeMethylationDataSpatialCorrelationcomputeMethylationProfilecomputeOverlapProfilecomputePMDscomputeVMDsfilterDMRsfilterPMDsfilterVMDsfilterVMRsONTgetWholeChromosomesjoinReplicatesmergeDMRsIterativelymergePMDsIterativelyplotLocalMethylationProfileplotMethylationDataCoverageplotMethylationDataSpatialCorrelationplotMethylationProfileplotMethylationProfileFromDataplotOverlapProfilepoolMethylationDatasetspoolTwoMethylationDatasetsreadBismarkreadBismarkPoolreadONTbamsaveBismarkselectCytosine

Dependencies:abindaskpassbetaregBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsBSgenomecigarilloclicodetoolscpp11crayoncurlDelayedArrayflexmixformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesgluehttrinflectionInteractionSetIRangesjsonlitelambda.rlatticelifecyclelmtestmagrittrMatrixMatrixGenericsmatrixStatsmimemodeltoolsnnetopensslR6RcppRcppRollRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssandwichSeqinfosnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzoo

Overview of the DMRcaller package

Nicolae Radu Zabet\thanks{e-mail: \texttt{[email protected]}, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK}

Rendered fromDMRcaller.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2025-10-17
Started: 2025-09-03

Readme and manuals

Help Manual

Help pageTopics
Analyse reads inside regions for conditionanalyseReadsInsideRegionsForCondition
Analyse reads inside regions for conditionanalyseReadsInsideRegionsForConditionPMD
Compute pairwise co-methylation statistics for cytosine sites within regionscomputeCoMethylatedPositions
Compute pairwise co-methylation statistics between regionscomputeCoMethylatedRegions
Compute DMRscomputeDMRs
Compute DMRscomputeDMRsReplicates
Compute methylation data coveragecomputeMethylationDataCoverage
Compute methylation data spatial correlationcomputeMethylationDataSpatialCorrelation
Compute methylation profilecomputeMethylationProfile
Compute Overlaps ProfilecomputeOverlapProfile
Compute PMDscomputePMDs
Compute VMDscomputeVMDs
Call Differentially Methylated Regions (DMRs) between two samplesDMRcaller-package DMRcaller
The DMRs between WT and met1-3 in CG contextDMRsNoiseFilterCG
Extract GCextractGC
Filter DMRsfilterDMRs
Filter PMDsfilterPMDs
Filter VMDsfilterVMDs
Filter VMRs for ONT DatafilterVMRsONT
The genetic elements dataGEs
The genetic elements data of GRCh38 Genome ReferenceGEs_hg38
Get whole chromosomes from methylation datagetWholeChromosomes
Joins together two GRange objects in a single containing all the replicatesjoinReplicates
Merge DMRs iterativelymergeDMRsIteratively
Merge PMDs iterativelymergePMDsIteratively
The methylation data listmethylationDataList
Partially Methilated Domains exampleont_gr_GM18870_chr1_PMD_bins_1k
The ONT methylation data exampleont_gr_GM18870_chr1_sorted_bins_1k
The ONT methylation data listontSampleGRangesList
Plot local methylation profileplotLocalMethylationProfile
Plot methylation data coverageplotMethylationDataCoverage
Plot methylation data spatial correlationplotMethylationDataSpatialCorrelation
Plot Methylation ProfileplotMethylationProfile
Plot methylation profile from dataplotMethylationProfileFromData
Plot overlap profileplotOverlapProfile
The PMDs between GM18501 and GM18876 using Bins methodPMDsBinsCG
The PMDs between GM18501 and GM18876 using Noise_filter methodPMDsNoiseFilterCG
Pool methylation datapoolMethylationDatasets
Pool two methylation datasetspoolTwoMethylationDatasets
Read BismarkreadBismark
Read Bismark poolreadBismarkPool
Load ONT BAM, decode MM/ML, and count modified vs. unmodified readsreadONTbam
Save BismarksaveBismark
The bam file from ONT nanopore .pod5 filesscanBamChr1Random5
Select Cytosine PositionsselectCytosine
Simulated data for biological replicatessyntheticDataReplicates