DESCRIPTION

Package: ECLIPSE
Title: Enhancer Calling and Linking with Integrated Profiling and Structure Evaluation
Version: 0.99.0.9000
Authors@R: c(
    person("Jared", "Andrews", , "jared.andrews07@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0780-6248")),
    person("Alyssa", "Obermayer", role = "aut"),
    person("Kelly", "McCastlain", role = "aut"),
    person("Jacqueline", "Myers", role = "aut"),
    person("Nicolas", "Peterson", role = "aut"),
    person("Young Lab - Whitehead Institute for Biomedical Research", role = "cph",
    comment = "Author of included original ROSE thresholding code."))
Description: ECLIPSE provides a performant implementation of the rank ordering of super enhancers (ROSE) method for identifying super enhancers.
    It provides options to increase the robustness of ROSE via signal transformations prior to thresholding and additional thresholding approaches.
    It increases flexibility and provides additional control by exposing parameters hidden in the original implementation.
    ECLIPSE also contains novel functionality to identify sub-structural changes within enhancer regions between groups via sliding window and binning approaches.
    ECLIPSE allows generation of high-quality plots of specific loci alongside arbitrary user-provided data.
URL: https://github.com/j-andrews7/ECLIPSE
BugReports: https://github.com/j-andrews7/ECLIPSE/issues
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports:
    BiocParallel,
    genomation,
    GenomicRanges,
    graphics,
    IRanges,
    Rsamtools,
    rtracklayer,
    S4Vectors,
    stats,
    KneeArrower,
    GenomeInfoDb,
    Gviz,
    csaw,
    stringi,
    data.table,
    MASS,
    ggplot2
Suggests:
    BiocStyle,
    knitr,
    testthat (>= 3.0.0),
    rmarkdown,
    BiocFileCache,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    org.Hs.eg.db,
    DESeq2,
    apeglm,
    segmented,
    ggrastr,
    plotly
Depends:
    R (>= 4.4.0)
biocViews: 
    Software,
    Sequencing,
    Visualization,
    MultipleComparison,
    Normalization,
    DifferentialPeakCalling,
    GeneRegulation,
    HistoneModification,
    PeakDetection,
    Epigenetics,
    ShinyApps,
    Classification
LazyData: false
Config/testthat/edition: 3
VignetteBuilder: knitr