TCGAbiolinks
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see TCGAbiolinks.
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Bioconductor version: 3.9
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: Antonio Colaprico <axc1833 at med.miami.edu>, Tiago Chedraoui Silva <tiagochst at usp.br>
citation("TCGAbiolinks")):
Installation
To install this package, start R (version "3.6") 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. TCGAbiolinks_Extension | 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) | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival |
| Version | 2.12.6 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.5) |
| Imports | downloader (>= 0.4), survminer, grDevices, dplyr, gridExtra, graphics, tibble, grid, GenomicRanges, XML (>= 3.98.0), data.table, EDASeq(>= 2.0.0), edgeR(>= 3.0.0), jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, ggthemes, survival, stringr (>= 1.0.0), IRanges, scales, rvest (>= 0.3.0), stats, utils, selectr, S4Vectors, ComplexHeatmap(>= 1.10.2), R.utils, SummarizedExperiment(>= 1.4.0), genefilter, ConsensusClusterPlus, readr, RColorBrewer, doParallel, GenomeInfoDb, GenomicFeatures, parallel, tools, tidyr, sva, limma, purrr, xml2, httr (>= 1.2.1), matlab, circlize, ggrepel (>= 0.6.3) |
| 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, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, igraph, supraHex |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | ELMER, miRLAB, MoonlightR, SingscoreAMLMutations, SpidermiR, TCGAbiolinksGUI, TCGAWorkflow |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TCGAbiolinks_2.12.6.tar.gz |
| Windows Binary | TCGAbiolinks_2.12.6.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | TCGAbiolinks_2.12.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TCGAbiolinks |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |