TCGAbiolinks

This is the development version of TCGAbiolinks; for the stable release version, see TCGAbiolinks.

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


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.33.0
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
See More
Suggests jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, 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, DT
Linking To
Enhances
Depends On Me
Imports Me ELMER, miRLAB, MoonlightR, SingscoreAMLMutations, SurfR, TCGAWorkflow
Suggests Me GeoTcgaData, iNETgrate, musicatk
Links To Me
Build Report Build Report

Package Archives

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

Source Package TCGAbiolinks_2.33.0.tar.gz
Windows Binary TCGAbiolinks_2.33.0.zip
macOS Binary (x86_64) TCGAbiolinks_2.33.0.tgz
macOS Binary (arm64)
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