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 (>= 4.6.0)
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
git_url: https://git.bioconductor.org/packages/CMEnt
git_branch: devel
git_last_commit: 6309a64
git_last_commit_date: 2026-10-19
Repository: Bioconductor 3.24
Date/Publication: 2026-10-20
Packaged: 2026-10-20 20:59:38 UTC; biocbuild
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>
