Package: MethReg
Type: Package
Title: Assessing the regulatory potential of DNA methylation regions or
        sites on gene transcription
Version: 1.18.0
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
git_url: https://git.bioconductor.org/packages/MethReg
git_branch: RELEASE_3_21
git_last_commit: cc9ab7e
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 02:02:36 UTC; biocbuild
Author: Tiago Silva [aut, cre] (ORCID: <https://orcid.org/0000-0003-1343-6850>),
  Lily Wang [aut]
Maintainer: Tiago Silva <tiagochst@gmail.com>
Built: R 4.5.0; ; 2025-04-16 14:51:31 UTC; windows
