DESCRIPTION

Package: TCGAutils
Title: TCGA utility functions for data management
Version: 1.27.0
Description: A suite of helper functions for checking and manipulating TCGA
  data including data obtained from the curatedTCGAData experiment package.
  These functions aim to simplify and make working with TCGA data more
  manageable. Exported functions include those that import data from flat files
  into Bioconductor objects, convert row annotations, and identifier
  translation via the GDC API.
Authors@R: c(
    person("Marcel", "Ramos", email = "marcel.ramos@sph.cuny.edu",
        role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3242-0582")),
    person("Lucas", "Schiffer", role = "aut"),
    person("Sean", "Davis", role = "ctb"),
    person("Levi", "Waldron", role = "aut")
    )
Depends:
    R (>= 4.2.0)
Imports:
    AnnotationDbi,
    BiocGenerics,
    BiocBaseUtils,
    GenomeInfoDb,
    GenomicFeatures,
    GenomicRanges,
    GenomicDataCommons,
    IRanges,
    methods,
    MultiAssayExperiment,
    RaggedExperiment (>= 1.5.7),
    rvest,
    S4Vectors,
    stats,
    stringr,
    SummarizedExperiment,
    utils,
    xml2
Suggests:
    AnnotationHub,
    BiocStyle,
    curatedTCGAData,
    ComplexHeatmap,
    devtools,
    dplyr,
    httr,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    impute,
    knitr,
    magrittr,
    mirbase.db,
    org.Hs.eg.db,
    RColorBrewer,
    readr,
    rmarkdown,
    RTCGAToolbox (>= 2.17.4),
    rtracklayer,
    R.utils,
    testthat,
    TxDb.Hsapiens.UCSC.hg18.knownGene,
    TxDb.Hsapiens.UCSC.hg19.knownGene
License: Artistic-2.0
Roxygen: list(markdown = TRUE)
Encoding: UTF-8
BugReports: https://github.com/waldronlab/TCGAutils/issues
biocViews: Software, WorkflowStep, Preprocessing, DataImport
VignetteBuilder: knitr
RoxygenNote: 7.3.0
Date: 2024-08-22