MethReg

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Bioconductor version: Release (3.20)

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")):

Installation

To install this package, start R (version "4.4") 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.

Documentation


Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Epigenetics, GeneExpression, GeneTarget, MethylationArray, Regression, Software, Transcription
Version	1.15.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
License	GPL-3
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
System Requirements
URL
Bug Reports	https://github.com/TransBioInfoLab/MethReg/issues/

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
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)	MethReg_1.15.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MethReg
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethReg
Bioc Package Browser	https://code.bioconductor.org/browse/MethReg/
Package Short Url	https://bioconductor.org/packages/MethReg/
Package Downloads Report	Download Stats