Package: CMEnt
Type: Package
Title: Characterization of Methylation using positional ENTanglement
Version: 0.99.15
Authors@R: c(
    person(given   = "Vasileios",
           family  = "Lemonidis",
           role    = c("aut", "cre", "cph"),
           email   = "vasileios.lemonidis@uantwerpen.be",
           comment = c(ORCID = "0000-0002-6446-3536")),
    person("Center for Oncological Research, University of Antwerp",
           role = c("cph", "fnd")),
    person("Stichting Tegen Kanker",
           role = "fnd"))
Description: 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.
URL: https://cmg-ua.github.io/CMEnt/, https://github.com/CMG-UA/CMEnt
BugReports: https://github.com/CMG-UA/CMEnt/issues
License: GPL (>= 2)
SystemRequirements: tabix, bgzip, GNU sort
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
biocViews: DNAMethylation, DifferentialMethylation, Epigenetics,
        StatisticalMethod, WorkflowStep, Annotation, MethylationArray,
        MotifAnnotation
Depends: R (>= 4.5.0)
Imports: AnnotationDbi, bedr, BiocGenerics, BiocFileCache,
        BiocParallel, Biostrings, BSgenome, bslib (>= 0.5.0), bsseq,
        callr, circlize, cli, colorspace, ComplexHeatmap, data.table,
        DelayedArray, DelayedDataFrame, DT, e1071, filelock, FNN,
        futile.logger, GenomeInfoDb, GenomicFeatures, GenomicRanges,
        ggplot2, ggseqlogo, graphics, grDevices, gridBase, gridExtra,
        HDF5Array, igraph, inline, IRanges, jsonlite, limma,
        matrixStats, methods, plotly, R.utils, R6, rhdf5, reshape2,
        rtracklayer, S4Vectors, shiny (>= 1.7.0), shinycssloaders,
        showtext, stats, strex, stringr, SummarizedExperiment,
        TFBSTools, tools, utils, withr
Suggests: bsseqData, DMRsegaldata, ExperimentHub, ggnewscale,
        IlluminaHumanMethylation27kanno.ilmn12.hg19,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
        IlluminaHumanMethylationEPICv2anno.20a1.hg38, BiocManager,
        devtools, DSS, knitr, pkgdown, rmarkdown, BiocStyle, magick,
        minfi, testthat (>= 3.0.0), mockery, DMRcate, doParallel,
        bumphunter, tidyr, scales, UpSetR,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hs1,
        BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39,
        org.Hs.eg.db, org.Mm.eg.db, JASPAR2024, optparse, pkgload
Config/testthat/edition: 3
Collate: 'annotate_dmrs_with_genes.R' 'augment_bsseq.R'
        'beta_handler.R' 'CMEnt-package.R' 'combine_pvalues.R'
        'convert_beta_to_tabix.R' 'dmrs_builder.R' 'dmrs_interaction.R'
        'find_dmps_array.R' 'find_dmps_bsseq.R' 'get_dmr_sequences.R'
        'load_example_input_data.R' 'plot_dmrs.R' 'plot_dmrs_circos.R'
        'read_custom_methylation_bed_data.R'
        'reduce_bsseq_around_seeds.R' 'shiny_app.R' 'shiny_modules.R'
        'score_dmrs.R' 'simulate_dmrs.R' 'sparsify_seeds.R'
        'sort_beta_file_by_coordinates.R' 'utils.R' 'zzz.R'
NeedsCompilation: no
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev make libgsl0-dev
        libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-19 22:47:04 UTC
RemoteUrl: https://github.com/bioc/CMEnt
RemoteRef: HEAD
RemoteSha: 6309a64fcfdc8f7d9be2b35bf9c3dc9594793756
Packaged: 2026-10-20 15:53:12 UTC; root
Author: Vasileios Lemonidis [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-6446-3536>),
  Center for Oncological Research, University of Antwerp [cph, fnd],
  Stichting Tegen Kanker [fnd]
Maintainer: Vasileios Lemonidis <vasileios.lemonidis@uantwerpen.be>