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Bioconductor - TCGAbiolinks (development version)

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 (3.22)

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 "4.5") 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")

Details biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival Version 2.37.1 In Bioconductor since BioC 3.2 (R-3.2) (9.5 years) License GPL (>= 3) Depends R (>= 4.1.0) 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, 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, MoonlightR, SurfR, TENET, CureAuxSP, oncoPredict 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.

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