MethReg
All Bioconductor versions of MethReg
3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
Bioconductor version: 3.23 · Package version: 1.21.0
Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.
Author: Tiago Silva [aut, cre] 
, Lily Wang [aut]
Maintainer: Tiago Silva <tiagochst at gmail.com>
Citation
From within R, enter citation("MethReg"):
Tiago Silva, Lily Wang. MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription. doi:10.18129/B9.bioc.MethReg, R package version 1.21.0, https://bioconductor.org/packages/MethReg.
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")
BiocManager::install("MethReg")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.21.0 |
| License | GPL-3 |
| Bug Reports | https://github.com/TransBioInfoLab/MethReg/issues/ |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| Status | Deprecated |
| Downloads rank | 1634 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Epigenetics, GeneExpression, GeneTarget, MethylationArray, Regression, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/MethReg/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | MethReg_1.21.0.tar.gz |
| Windows binary (x86_64) | MethReg_1.21.1.zip |
| macOS binary (arm64) | MethReg_1.21.0.tgz |
| macOS binary (x86_64) | MethReg_1.21.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MethReg |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MethReg |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.0)
Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite, TFBSTools
Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils, doParallel, reshape2, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, data.table, downloader