TCGAbiolinks

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TCGAbiolinks.

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Bioconductor version: 3.16

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.

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 at gmail.com>, Antonio Colaprico <axc1833 at med.miami.edu>

Citation (from within R, enter citation("TCGAbiolinks")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TCGAbiolinks")

1. Introduction HTML R Script

10. Classifiers HTML R Script

10. TCGAbiolinks_Extension HTML R Script

11. Stemness score HTML R Script

2. Searching GDC database HTML R Script

3. Downloading and preparing files for analysis HTML R Script

4. Clinical data HTML R Script

5. Mutation data HTML R Script

6. Compilation of TCGA molecular subtypes HTML R Script

7. Analyzing and visualizing TCGA data HTML R Script

8. Case Studies HTML R Script

9. Graphical User Interface (GUI) HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival

Version 2.25.3

In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)

License GPL (>= 3)

Depends R (>= 4.0)

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)

System Requirements

URL https://github.com/BioinformaticsFMRP/TCGAbiolinks

Bug Reports https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues