MethReg
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
Bioconductor version: Release (3.19)
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("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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MethReg")| MethReg: estimating regulatory potential of DNA methylation in gene transcription | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Epigenetics, GeneExpression, GeneTarget, MethylationArray, Regression, Software, Transcription |
| Version | 1.14.0 |
| 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/ |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MethReg_1.14.0.tar.gz |
| Windows Binary (x86_64) | MethReg_1.14.0.zip |
| macOS Binary (x86_64) | MethReg_1.14.0.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 |