TCGAbiolinks

DOI: 10.18129/B9.bioc.TCGAbiolinks  

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

Bioconductor version: Release (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>

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")

 

HTML	R Script	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)
PDF		Reference Manual
Text		NEWS

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) (7.5 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)
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/BioinformaticsFMRP/TCGAbiolinks
BugReports	https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues
Depends On Me
Imports Me	ELMER, miRLAB, MoonlightR, musicatk, SingscoreAMLMutations, TCGAbiolinksGUI, TCGAWorkflow
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TCGAbiolinks_2.25.3.tar.gz
Windows Binary	TCGAbiolinks_2.26.0.zip
macOS Binary (x86_64)	TCGAbiolinks_2.26.0.tgz
macOS Binary (arm64)	TCGAbiolinks_2.25.3.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