Package: MethReg
Type: Package
Title: Assessing the regulatory potential of DNA methylation regions or
        sites on gene transcription
Version: 1.20.0
Authors@R: c(
    person("Tiago", "Silva", email = "tiagochst@gmail.com", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0003-1343-6850")),
    person("Lily", "Wang", email = "lily.wangg@gmail.com", role = c("aut"))
      )
Description: 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.
License: GPL-3
Encoding: UTF-8
LazyData: true
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
VignetteBuilder: knitr
BugReports: https://github.com/TransBioInfoLab/MethReg/issues/
RoxygenNote: 7.3.1
Depends: R (>= 4.0)
biocViews: MethylationArray, Regression, GeneExpression, Epigenetics,
        GeneTarget, Transcription
Config/pak/sysreqs: cmake make libgsl0-dev libbz2-dev libicu-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:02:28 UTC
RemoteUrl: https://github.com/bioc/MethReg
RemoteRef: RELEASE_3_22
RemoteSha: a1982d565ec558d3d6883b74ce4d0e5e2b28c63c
NeedsCompilation: no
Packaged: 2025-11-11 21:22:34 UTC; root
Author: Tiago Silva [aut, cre] (ORCID: <https://orcid.org/0000-0003-1343-6850>),
  Lily Wang [aut]
Maintainer: Tiago Silva <tiagochst@gmail.com>
Built: R 4.5.2; ; 2025-11-12 03:25:56 UTC; windows
