Package: REMP
Type: Package
Title: Repetitive Element Methylation Prediction
Version: 1.35.0
Authors@R: c(person("Yinan","Zheng", role = c("aut","cre"), email = "y-zheng@northwestern.edu"),person("Lei","Liu", role = c("aut"), email = "lei.liu@northwestern.edu "), person("Wei","Zhang", role = c("aut"), email = "wei.zhang1@northwestern.edu"), person("Warren","Kibbe", role = c("aut"), email = "warren.kibbe@nih.gov"), person("Lifang","Hou", role = c("aut","cph"), email = "l-hou@northwestern.edu"))
Description: Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. 
License: GPL-3
Depends:
    R (>= 3.6),
    SummarizedExperiment(>= 1.1.6),
    minfi (>= 1.22.0)
Imports:
    readr,
    rtracklayer,
    graphics,
    stats,
    utils,
    methods,
    settings,
    BiocGenerics,
    S4Vectors,
    Biostrings,
    GenomicRanges,
    IRanges,
    Seqinfo,
    BiocParallel,
    doParallel,
    parallel,
    foreach,
    caret,
    kernlab,
    ranger,
    BSgenome,
    AnnotationHub,
    org.Hs.eg.db,
    impute,
    iterators
Suggests:
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
    BSgenome.Hsapiens.UCSC.hg19,
    BSgenome.Hsapiens.UCSC.hg38,
    knitr,
    rmarkdown,
    minfiDataEPIC
Collate:
    REMParcel-class.R
    REMProduct-class.R
    generics.R
    REMParcel-methods.R
    REMProduct-methods.R
    options.R
    utils.R
    REMPtools.R
    getGM12878.R
    grooMethy.R
    initREMP.R
    rempTemplate.R
    remp.R
    remprofile.R
    DemoData.R
    onAttach.R
    REMP-package.R
URL: https://github.com/YinanZheng/REMP
BugReports: https://github.com/YinanZheng/REMP/issues
Encoding: UTF-8
LazyData: true
biocViews: 
    DNAMethylation, 
    Microarray, 
    MethylationArray, 
    Sequencing,
    GenomeWideAssociation,
    Epigenetics, 
    Preprocessing, 
    MultiChannel, 
    TwoChannel, 
    DifferentialMethylation, 
    QualityControl, 
    DataImport
RoxygenNote: 7.1.2
git_url: https://git.bioconductor.org/packages/REMP
git_branch: devel
git_last_commit: 6cbaa64
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
