CMEnt

This is the development version of CMEnt; to use it, please install the devel version of Bioconductor.

Characterization of Methylation using positional ENTanglement

Bioconductor version: Development (3.24)

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.

Author: Vasileios Lemonidis [aut, cre, cph] ORCID: 0000-0002-6446-3536 , Center for Oncological Research, University of Antwerp [cph, fnd], Stichting Tegen Kanker [fnd]

Maintainer: Vasileios Lemonidis <vasileios.lemonidis at uantwerpen.be>

Citation (from within R, enter citation("CMEnt")):

Vasileios Lemonidis. CMEnt: Characterization of Methylation using positional ENTanglement. doi:10.18129/B9.bioc.CMEnt, R package version 0.99.15, https://bioconductor.org/packages/CMEnt.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("CMEnt")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CMEnt")

CMEnt Configuration	HTML
CMEnt End-to-End Example	HTML
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DNAMethylation, DifferentialMethylation, Epigenetics, MethylationArray, MotifAnnotation, Software, StatisticalMethod, WorkflowStep
Version	0.99.15
In Bioconductor since	BioC 3.24 (R-4.6)
License	GPL (>= 2)
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
System Requirements	tabix, bgzip, GNU sort
URL	https://cmg-ua.github.io/CMEnt/ https://github.com/CMG-UA/CMEnt
Bug Reports	https://github.com/CMG-UA/CMEnt/issues

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
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CMEnt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CMEnt
Package Short Url	https://bioconductor.org/packages/CMEnt/
Package Downloads Report	Download Stats