Package: CMEnt 0.99.13

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_0.99.13.tar.gz
CMEnt_0.99.13.zip(r-4.7-any)CMEnt_0.99.13.zip(r-4.6-any)CMEnt_0.99.13.zip(r-4.5-any)
CMEnt_0.99.13.tgz(r-4.6-any)CMEnt_0.99.13.tgz(r-4.5-any)
CMEnt_0.99.13.tar.gz(r-4.7-any)CMEnt_0.99.13.tar.gz(r-4.6-any)
CMEnt_0.99.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
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

4.65 score 17 scripts 29 exports 194 dependencies

Last updated from:3bcc0a65b0. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING1707
linux-develOK2279
source / vignettesOK2040
linux-releaseOK2072
macos-releaseOK2011
macos-oldrelOK2106
windows-develOK2044
windows-releaseOK2079
windows-oldrelOK2089
wasm-releaseOK1728

Exports:annotateDMRsWithGenesaugmentBSSeqbuildDMRscombinePvaluescomputeDMRsInteractionconvertBetaToTabixextractDMRMotifsfindDMPsArrayfindDMPsBSSeqgetBetaHandlergetDMRSequencesgetSortedGenomicLocslaunchCMEntViewerloadExampleInputDataloadExampleInputDataChr21And22loadExampleInputDataChr5And11orderByLocplotAutoDMRsCircosplotDMRplotDMRBlockFormationplotDMRsplotDMRsCircosplotDMRsManhattanreadCustomMethylationBedDatareduceBSseqAroundSeedsscoreDMRssimulateDMRssortBetaFileByCoordinatessparsifySeeds

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

CMEnt Configuration
Introduction | Installation | Function Parameters | Core Input Parameters | beta | seeds | pheno | Sample Grouping Parameters | sample_group_col | casecontrol_col | ignored_sample_groups | Array and Genome Parameters | array | genome | Filtering Parameters | ext_site_delta_beta | min_seeds | min_adj_seeds | min_sites | Region Building Parameters | max_lookup_dist | expansion_window | max_bridge_seeds_gaps | max_bridge_extension_gaps | Statistical Parameters | max_pval | entanglement | testing_mode | empirical_strategy | ntries | mid_p | aggfun | Performance Parameters | njobs | verbose | Input/Output Parameters | seeds_id_col | output_prefix | beta_row_names_file | BED File Parameters | bed_provided | bed_chrom_col | bed_start_col | Annotation Parameters | annotate_with_genes | score_dmrs | Advanced Parameters | .load_debug | Global Package Options | Parallelism | Option: CMEnt.njobs | Verbosity | Option: CMEnt.verbose | Memory Management | Option: CMEnt.beta_in_mem_threshold_mb | Caching | Option: CMEnt.use_annotation_cache | Option: CMEnt.annotation_cache_dir | Option: CMEnt.jaspar_cache_dir | Motif Analysis | Option: CMEnt.jaspar_version | Option: CMEnt.jaspar_tax_group | Option: CMEnt.min_motif_similarity | Option: CMEnt.jaspar_corr_threshold | Option: CMEnt.make_debug_dir | DMR scoring | Option: CMEnt.scoring_nfold | Configuration Examples | Example 1: High-Confidence DMRs with Strict Filtering | Example 2: Broad Region Detection with Relaxed Parameters | Example 3: Empirical P-values for Small Sample Sizes | Best Practices | Troubleshooting | Issue: Out of Memory Errors | Issue: DMRs Too Small | Issue: Too Many DMRs | Issue: Slow Performance | Session Info
Rendered fromconfiguration.Rmdusingknitr::rmarkdown

Last update: 2026-10-18
Started: 2025-11-06

CMEnt End-to-End Example
Introduction | Installation | Setup | Load Example Inputs | DMR Assembly from Seeds | DMR Summary | Motif Discovery | Motif-Based DMR Interactions | Visualizations | DMR Score Manhattan Plot | Single DMR Plot | Summary Circos Plot | CMEnt interactive Shiny App | Session Info
Rendered fromcment_example.Rmdusingknitr::rmarkdown

Last update: 2026-10-18
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
Reduce BSseq object around seed locationsreduceBSseqAroundSeeds
Add Complementary Classification Scores to DMRsscoreDMRs
Simulate DMRs while preserving local methylation structuresimulateDMRs
Sort Beta File by Genomic CoordinatessortBetaFileByCoordinates
Sparsify seed locations by minimum distancesparsifySeeds