TCGAbiolinks

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

Bioconductor version: Release (3.17)

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 "4.3") 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
Reference Manual	PDF
NEWS	Text

Details

biocViews	DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival
Version	2.28.3
In Bioconductor since	BioC 3.2 (R-3.2) (8 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)
Linking To
Suggests	jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid
System Requirements
Enhances
URL	https://github.com/BioinformaticsFMRP/TCGAbiolinks
Bug Reports	https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues

Depends On Me
Imports Me	ELMER, miRLAB, MoonlightR, SingscoreAMLMutations, TCGAWorkflow
Suggests Me	GeoTcgaData, musicatk
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	TCGAbiolinks_2.28.3.tar.gz
Windows Binary	TCGAbiolinks_2.28.3.zip
macOS Binary (x86_64)	TCGAbiolinks_2.28.3.tgz
macOS Binary (arm64)	TCGAbiolinks_2.27.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TCGAbiolinks
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TCGAbiolinks
Bioc Package Browser	https://code.bioconductor.org/browse/TCGAbiolinks/
Package Short Url	https://bioconductor.org/packages/TCGAbiolinks/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive