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]
, Center for Oncological Research, University of Antwerp [cph, fnd], Stichting Tegen Kanker [fnd]
Maintainer: Vasileios Lemonidis <vasileios.lemonidis at uantwerpen.be>
citation("CMEnt")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | R Script |
| CMEnt End-to-End Example | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text |
Details
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CMEnt_0.99.15.tar.gz |
| Windows Binary (x86_64) | CMEnt_0.99.15.zip |
| macOS Binary (big-sur-x86_64) | CMEnt_0.99.15.tgz |
| macOS Binary (sonoma-arm64) | CMEnt_0.99.15.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CMEnt |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CMEnt |
| Bioc Package Browser | https://code.bioconductor.org/browse/CMEnt/ |
| Package Short Url | https://bioconductor.org/packages/CMEnt/ |
| Package Downloads Report | Download Stats |