Package: RLSeq
Type: Package
Title: RLSeq: An analysis package for R-loop mapping data
Version: 1.9.0
Authors@R: c(
    person(given = "Henry",
           family = "Miller",
           role = c("aut", "cre", "cph"),
           email = "millerh1@uthscsa.edu",
           comment = c(ORCID = "0000-0003-3756-3918")),
    person(given = "Daniel",
           family = "Montemayor",
           role = c("ctb"),
           comment = c(ORCID = "0000-0001-8702-5646")),
    person(given = "Simon",
           family = "Levy",
           role = c("ctb"),
           comment = c(ORCID = "0000-0002-4623-5716")),
    person(given = "Anna",
           family = "Vines",
           comment = c(ORCID = "0000-0002-5149-7737"),
           role = c("ctb")),
    person(given = "Alexander",
           family = "Bishop",
           email = "bishopa@uthscsa.edu",
           comment = c(ORCID = "0000-0002-5742-4387"),
           role = c("ths", "cph")))
Description: RLSeq is a toolkit for analyzing and evaluating R-loop mapping datasets.
    RLSeq serves two primary purposes: (1) to facilitate the evaluation of dataset quality, and
    (2) to enable R-loop analysis in the context of publicly-available data sets from RLBase.
    The package is intended to provide a simple pipeline, called with the `RLSeq()` function, 
    which performs all main analyses. Individual functions are also accessible and provide custom
    analysis capabilities. Finally an HTML report is generated with `report()`. 
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
Suggests: 
    AnnotationDbi,
    BiocStyle,
    covr,
    lintr,
    rcmdcheck,
    DT,
    httr,
    jsonlite,
    kableExtra,
    kernlab,
    knitr,
    magick,
    MASS,
    org.Hs.eg.db,
    R.utils,
    randomForest,
    readr,
    rmarkdown,
    rpart,
    testthat (>= 3.0.0),
    tibble,
    tidyr,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    futile.logger
Config/testthat/edition: 3
Depends: 
    R (>= 4.2.0)
Imports: 
    dplyr,
    ggplot2,
    RColorBrewer,
    grid,
    regioneR,
    valr,
    caretEnsemble,
    GenomicFeatures,
    rtracklayer,
    GenomicRanges,
    GenomeInfoDb,
    ComplexHeatmap,
    AnnotationHub,
    VennDiagram,
    callr,
    circlize,
    ggplotify,
    ggprism,
    methods,
    stats,
    RLHub,
    aws.s3,
    pheatmap
VignetteBuilder: knitr
biocViews: Sequencing, Coverage, Epigenetics, Transcriptomics, Classification
URL: https://github.com/Bishop-Laboratory/RLSeq, https://bishop-laboratory.github.io/RLSeq/
BugReports: https://github.com/Bishop-Laboratory/RLSeq/issues
BiocType: Software