MethReg

DOI: 10.18129/B9.bioc.MethReg    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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

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

browseVignettes("MethReg")

 

HTML	R Script	MethReg: estimating regulatory potential of DNA methylation in gene transcription
PDF		Reference Manual
Text		NEWS

Details

biocViews	Epigenetics, GeneExpression, GeneTarget, MethylationArray, Regression, Software, Transcription
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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
LinkingTo
Suggests	rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2020, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
BugReports	https://github.com/TransBioInfoLab/MethReg/issues/
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	MethReg_1.6.0.tar.gz
Windows Binary	MethReg_1.6.0.zip
macOS Binary (x86_64)	MethReg_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MethReg
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethReg
Package Short Url	https://bioconductor.org/packages/MethReg/
Package Downloads Report	Download Stats