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>

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")

 

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

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