MethProScan/DESCRIPTION at main · lucianhu/MethProScan · GitHub

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Package: MethProScan
Title: Methylation Analysis with Promoter Region Scanning
Version: 1.0.0
Date: 2024-10-28
Authors@R:
    person("Quynh Nhu", "Nguyen", , "lucianhu@gmail.com", role = c("aut", "cre"))
Description: Provides comprehensive tools for DNA methylation array data analysis
    with a focus on promoter regions. Performs differential methylation analysis
    at both the CpG (DMC) and regional (DMR) levels with statistical testing.
    Includes general statistical analysis functions for methylation data exploration
    and quality assessment. Supports custom region definitions with specialized
    functions for promoter region analysis. Includes liftover capabilities to
    convert Illumina EPIC v2 array data to EPIC v1 coordinates for cross-platform
    compatibility and integration with existing datasets. Offers visualization
    functions to explore and present methylation patterns and statistical results.
    Streamlines methylation data processing workflows from array data to
    biologically meaningful results.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
biocViews: DNAMethylation, MethylationArray, Microarray,
    Preprocessing, Normalization, QualityControl,
    DifferentialMethylation, GenomeAnnotation,
    Epigenetics, StatisticalMethod, Regression,
    Visualization, CopyNumberVariation, Promoter
Suggests:
    bumphunter,
    DMRcate,
    EnhancedVolcano,
    harmonicmeanp,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    IlluminaHumanMethylation450kmanifest,
    IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
    IlluminaHumanMethylationEPICanno.ilm10b5.hg38 (>= 0.0.1),
    IlluminaHumanMethylationEPICmanifest (>= 0.3.0),
    IlluminaHumanMethylationEPICv2manifest,
    mCSEA (>= 1.27.2),
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports:
    affy,
    BiocManager,
    BiocParallel,
    circlize,
    ComplexHeatmap,
    dplyr,
    GenomicRanges,
    ggplot2,
    ggrepel,
    graphics,
    grDevices,
    grid,
    htmlwidgets,
    limma,
    maxprobes (>= 0.0.2),
    methods,
    minfi,
    plotly,
    remotes,
    rlang,
    Rtsne,
    S4Vectors,
    scales,
    sesame,
    stats,
    SummarizedExperiment,
    sva,
    tibble,
    tidyr,
    tools,
    utils,
    uwot,
    wateRmelon
Remotes:
    markgene/maxprobes,
    achilleasNP/IlluminaHumanMethylationEPICmanifest,
    achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38,
    jordimartorell/mCSEA