Package: TCGAbiolinks
Type: Package
Title: TCGAbiolinks: An R/Bioconductor package for integrative analysis
        with GDC data
Version: 2.39.0
Date: 2024-01-01
Author: Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen,
        Luciano Garofano, Davide Garolini, Claudia Cava, Thais Sabedot,
        Tathiane Malta, Stefano M. Pagnotta, Isabella Castiglioni,
        Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr
Maintainer: Tiago Chedraoui Silva <tiagochst@gmail.com>, Antonio
 Colaprico <axc1833@med.miami.edu>
Depends: R (>= 4.1.0)
Imports: downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics,
        tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite
        (>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0),
        IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils,
        SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>=
        1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1)
Description: The aim of TCGAbiolinks is : i) facilitate the GDC
        open-access data retrieval, ii) prepare the data using the
        appropriate pre-processing strategies, iii) provide the means
        to carry out different standard analyses and iv) to easily
        reproduce earlier research results. In more detail, the package
        provides multiple methods for analysis (e.g., differential
        expression analysis, identifying differentially methylated
        regions) and methods for visualization (e.g., survival plots,
        volcano plots, starburst plots) in order to easily develop
        complete analysis pipelines.
License: GPL (>= 3)
biocViews: DNAMethylation, DifferentialMethylation, GeneRegulation,
        GeneExpression, MethylationArray, DifferentialExpression,
        Pathways, Network, Sequencing, Survival, Software
Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools,
        parmigene, c3net, minet, Biobase, affy, testthat, sesame,
        AnnotationHub, ExperimentHub, pathview, clusterProfiler,
        Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph,
        limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra,
        survival, doParallel, parallel, ggrepel (>= 0.6.3), scales,
        grid, DT
VignetteBuilder: knitr
LazyData: true
URL: https://github.com/BioinformaticsFMRP/TCGAbiolinks
BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues
RoxygenNote: 7.3.3
Encoding: UTF-8
Config/pak/sysreqs: libicu-dev libpng-dev libxml2-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:27:16 UTC
RemoteUrl: https://github.com/bioc/TCGAbiolinks
RemoteRef: HEAD
RemoteSha: 2072af1a0a91b799e0a6e9d5dd5c0eed37c15704
NeedsCompilation: no
Packaged: 2025-12-12 08:03:30 UTC; root
Built: R 4.6.0; ; 2025-12-12 08:07:03 UTC; windows
