Package: CMEnt 0.99.3

Vasileios Lemonidis

CMEnt: Characterization of Methylation using positional ENTanglement

CMEnt implements a correlation-based method for identifying Differentially Methylated Regions (DMRs) from genomic seeds, commonly Differentially Methylated Positions (DMPs). The package expands regions around significant seeds considering both statistical significance and biological relevance of methylation changes. It supports array-based (450K, EPIC, EPICv2) and NGS methylation data through tabix-indexed files, provides DMR interaction analysis via motif similarity, and includes comprehensive visualization tools including circos plots and beta value heatmaps.

Authors:Vasileios Lemonidis [aut, cre, cph], Center for Oncological Research, University of Antwerp [cph, fnd], Stichting Tegen Kanker [fnd]

CMEnt_0.99.3.tar.gz
CMEnt_0.99.3.zip(r-4.7)CMEnt_0.99.3.zip(r-4.6)CMEnt_0.99.3.zip(r-4.5)
CMEnt_0.99.3.tgz(r-4.6-any)CMEnt_0.99.3.tgz(r-4.5-any)
CMEnt_0.99.3.tar.gz(r-4.7-any)CMEnt_0.99.3.tar.gz(r-4.6-any)
CMEnt_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CMEnt/json (API)

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

Bug tracker:https://github.com/cmg-ua/cment/issues

Pkgdown/docs site:https://cmg-ua.github.io

On CRAN:

Conda:

dnamethylationdifferentialmethylationepigeneticsstatisticalmethodworkflowstepannotationmethylationarraymotifannotation

4.46 score 17 scripts 27 exports 195 dependencies

Last updated from:068736f8e6. Checks:1 NOTE, 7 ERROR, 2 OK. Indexed: yes.
A new build is currently in progress.

TargetResultTimeFilesSyslog
bioc-checksNOTE1677
linux-devel-x86_64ERROR2928
source / vignettesOK2090
linux-release-x86_64ERROR2764
macos-release-arm64ERROR3372
macos-oldrel-arm64ERROR3076
windows-develERROR2918
windows-releaseERROR2997
windows-oldrelERROR2459
wasm-releaseOK1852

Exports:annotateDMRsWithGenesaugmentBSSeqbuildDMRscombinePvaluescomputeDMRsInteractionconvertBetaToTabixextractDMRMotifsfindDMPsArrayfindDMPsBSSeqgetBetaHandlergetDMRSequencesgetSortedGenomicLocslaunchCMEntViewerloadExampleInputDataloadExampleInputDataChr21And22loadExampleInputDataChr5And11orderByLocplotAutoDMRsCircosplotDMRplotDMRBlockFormationplotDMRsplotDMRsCircosplotDMRsManhattanreadCustomMethylationBedDatascoreDMRssimulateDMRssortBetaFileByCoordinates

Dependencies:abindAnnotationDbiaskpassassortheadbackportsbase64encbeachmatbedrBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbrioBSgenomebslibbsseqcachemcallrcaToolscheckmatecigarillocirclizeclasscliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedDataFrameDelayedMatrixStatsdescdiffobjdigestdir.expiryDirichletMultinomialdoParalleldplyrDTe1071evaluatefarverfastmapfilelockFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggseqlogoGlobalOptionsgluegridBasegridExtragtablegtoolsh5mreadHDF5Arrayhighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphinlineIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpermutepillarpkgbuildpkgconfigpkgloadplotlyplyrpngpraiseprocessxpromisesproxypspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesSeqinfoseqLogoshapeshinyshinycssloadersshowtextshowtextdbsnowsourcetoolsSparseArraysparseMatrixStatsstatmodstrexstringistringrSummarizedExperimentsyssysfontstestthatTFBSToolsTFMPvaluetibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsVennDiagramviridisLitewaldowithrxfunXMLxtableXVectoryaml

CMEnt Configuration

CMEnt Package

Rendered fromconfiguration.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-06-10
Started: 2025-11-06

CMEnt End-to-End Example

CMEnt Package

Rendered fromcment_example.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-06-11
Started: 2026-04-23

Readme and manuals

Help Manual

Help pageTopics
Annotate DMRs with Gene InformationannotateDMRsWithGenes
Augment BSseq ObjectaugmentBSSeq
Build Differentially Methylated Regions (DMRs) from Differentially Methylated Positions (seeds)buildDMRs
Combine spatially correlated p-values with comb-p style SLK correctioncombinePvalues
Compute Motif-Based DMR InteractionscomputeDMRsInteraction
Convert Beta File to Tabix-Indexed FormatconvertBetaToTabix
Extract DMR Motif FrequenciesextractDMRMotifs
Find DMPs from methylation array beta values using limmafindDMPsArray
Find DMPs using DSS on BSseq objectsfindDMPsBSSeq
Create a BetaHandler object for efficient beta value accessgetBetaHandler
Extract DNA Sequences for DMRsgetDMRSequences
Get Sorted Array LocationsgetSortedGenomicLocs
Launch CMEnt Interactive ViewerlaunchCMEntViewer
Load CMEnt Example ResourcesloadExampleInputData loadExampleInputDataChr21And22 loadExampleInputDataChr5And11
Orders a vector of indices according to their corresponding genomic locations (chromosome and position). This function is useful for sorting site sites or other genomic features by their physical positions.orderByLoc
Plot DMR Circos Views Using Automatically Selected RegionsplotAutoDMRsCircos
Plot DMRplotDMR
Plot Intermediate DMR Block Formation DiagnosticsplotDMRBlockFormation
Plot Multiple DMRs in a GridplotDMRs
Plot Circos Visualization of DMRsplotDMRsCircos
Plot Manhattan-Style View of DMR ScoresplotDMRsManhattan
Read and Process Custom Methylation BED DatareadCustomMethylationBedData
Add Complementary Classification Scores to DMRsscoreDMRs
Simulate DMRs while preserving local methylation structuresimulateDMRs
Sort Beta File by Genomic CoordinatessortBetaFileByCoordinates