MethReg

DOI: 10.18129/B9.bioc.MethReg    

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

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0)
Imports dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress
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
SystemRequirements
Enhances
URL
BugReports https://github.com/TransBioInfoLab/MethReg/issues/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MethReg_1.0.0.tar.gz
Windows Binary MethReg_1.0.0.zip
macOS 10.13 (High Sierra) MethReg_1.0.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: