Package: TCGAutils
Title: TCGA utility functions for data management
Version: 1.33.3
Date: 2026-07-02
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", , "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"),
    person("NCI", role = "fnd",
           comment = c(GrantNo. = "U24CA289073"))
  )
Depends: R (>= 4.5.0)
Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb,
        GenomicFeatures, GenomicRanges, GenomicDataCommons, glue,
        IRanges, methods, MultiAssayExperiment, RaggedExperiment,
        rvest, S4Vectors, Seqinfo, stats, stringr,
        SummarizedExperiment, utils, xml2
Suggests: AnnotationHub, Bioc.gff, BiocFileCache, BiocStyle,
        curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr,
        IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr,
        magrittr, miRNAmeConverter, org.Hs.eg.db, RColorBrewer, readr,
        rmarkdown, RTCGAToolbox, 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
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-02 19:16:56 UTC
RemoteUrl: https://github.com/bioc/TCGAutils
RemoteRef: HEAD
RemoteSha: 48aa352190750354aaa86e51bcab53879beda79b
NeedsCompilation: no
Packaged: 2026-07-02 22:00:11 UTC; root
Author: Marcel Ramos [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3242-0582>),
  Lucas Schiffer [aut],
  Sean Davis [ctb],
  Levi Waldron [aut],
  NCI [fnd] (GrantNo.: U24CA289073)
Maintainer: Marcel Ramos <marcel.ramos@sph.cuny.edu>