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TCGAbiolinks R/Bioconductor Package

repository·master·Indexed 43 days ago

https://github.com/bioinformaticsfmrp/tcgabiolinks

An R/Bioconductor package providing a programmatic interface to the NCI Genomic Data Commons (GDC) API. It enables users to search, download, and prepare TCGA (The Cancer Genome Atlas) data for integrative cancer genomics analysis.

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What's inside TCGAbiolinks

  1. Overview of TCGAbiolinks

    master

    TCGAbiolinks is an R/Bioconductor package designed for integrative analysis with TCGA (The Cancer Genome Atlas) data. It interfaces with the National Cancer Institute (NCI) Genomic Data Commons (GDC) API to:

    • Search for relevant genomic data.
    • Download data from the GDC.
    • Prepare data for downstream analysis within the R environment.

  2. Install TCGAbiolinks from Bioconductor

    master

    The recommended way to install TCGAbiolinks is via Bioconductor using BiocManager. This ensures compatibility with the Bioconductor ecosystem.

    if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TCGAbiolinks")

  4. Install TCGAbiolinks from GitHub

    master

    To install the development version or specific GitHub versions, use BiocManager::install pointing to the BioinformaticsFMRP repository. Note that you may also need to install TCGAbiolinksGUI.data if working with the GUI components.

    if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")