Package: RLSeq
Type: Package
Title: RLSeq: An analysis package for R-loop mapping data
Version: 1.2.0
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: 7.1.2
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 (>= 4.1.0)
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
git_url: https://git.bioconductor.org/packages/RLSeq
git_branch: RELEASE_3_15
git_last_commit: 7afa0ea
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
NeedsCompilation: no
Packaged: 2022-04-27 00:54:16 UTC; biocbuild
Author: Henry Miller [aut, cre, cph] (<https://orcid.org/0000-0003-3756-3918>),
  Daniel Montemayor [ctb] (<https://orcid.org/0000-0001-8702-5646>),
  Simon Levy [ctb] (<https://orcid.org/0000-0002-4623-5716>),
  Anna Vines [ctb] (<https://orcid.org/0000-0002-5149-7737>),
  Alexander Bishop [ths, cph] (<https://orcid.org/0000-0002-5742-4387>)
Maintainer: Henry Miller <millerh1@uthscsa.edu>
Built: R 4.2.0; ; 2022-04-27 10:00:33 UTC; windows
