Package: RTCGAToolbox
Type: Package
Title: A new tool for exporting TCGA Firehose data
Version: 2.39.0
Authors@R: c(
    person("Mehmet", "Samur", email = "rtcgatoolbox@gmail.com",
    role = "aut"),
    person("Marcel", "Ramos", email = "marcel.ramos@sph.cuny.edu",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3242-0582")),
    person("Ludwig", "Geistlinger", role = "ctb"))
Description: Managing data from large scale projects such as The Cancer
        Genome Atlas (TCGA) for further analysis is an important and
        time consuming step for research projects. Several efforts,
        such as Firehose project, make TCGA pre-processed data publicly
        available via web services and data portals but it requires
        managing, downloading and preparing the data for following
        steps. We developed an open source and extensible R based data
        client for Firehose pre-processed data and demonstrated its use
        with sample case studies. Results showed that RTCGAToolbox
        could improve data management for researchers who are
        interested with TCGA data. In addition, it can be integrated
        with other analysis pipelines for following data analysis.
License: GPL-2
Depends: R (>= 4.3.0)
Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges,
        GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO,
        rvest, S4Vectors, stats, stringr, SummarizedExperiment,
        TCGAutils, utils
Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
biocViews: DifferentialExpression, GeneExpression, Sequencing
URL: http://mksamur.github.io/RTCGAToolbox/
BugReports: https://github.com/mksamur/RTCGAToolbox/issues
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Collate: 'RTCGAToolbox-Class.R' 'RTCGAToolbox.R' 'utils.R'
        'biocExtract.R' 'data.R' 'getBroadSubtypes.R'
        'getFirehoseAnalyzeDates.R' 'getFirehoseData.R'
        'getFirehoseDatasets.R' 'getFirehoseRunningDates.R'
        'getGISTICPeaks.R' 'getLinks.R' 'getMutationRate.R'
        'makeSummarizedExperimentFromGISTIC.R' 'selectType.R'
Encoding: UTF-8
Date: 2024-12-18
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://link-ny.r-universe.dev
Date/Publication: 2025-04-15 14:51:14 UTC
RemoteUrl: https://github.com/mksamur/RTCGAToolbox
RemoteRef: HEAD
RemoteSha: 505739c59f2f073646fbf4e20c875681fe95c342
NeedsCompilation: no
Packaged: 2026-07-02 21:45:59 UTC; root
Author: Mehmet Samur [aut],
  Marcel Ramos [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3242-0582>),
  Ludwig Geistlinger [ctb]
Maintainer: Marcel Ramos <marcel.ramos@sph.cuny.edu>