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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")
In most cases, you don't need to download the package archive at all.
TCGAbiolinks
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see TCGAbiolinks.
TCGAbiolinks: An R/Bioconductor package for integrative analysis with TCGA data
Bioconductor version: 3.2
The aim of TCGAbiolinks is : i) facilitate the TCGA 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) allow the user to download a specific version of the data and thus 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 M. Malta, Stefano M. Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr
Maintainer: Antonio Colaprico <antonio.colaprico at ulb.ac.be>, Tiago Chedraoui Silva <tiagochst at usp.br>
Citation (from within R,
enter citation("TCGAbiolinks")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TCGAbiolinks")
| HTML | Working with TCGAbiolinks package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Software, Survival |
| Version | 1.0.10 |
| In Bioconductor since | BioC 3.2 (R-3.2) (0.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.2) |
| Imports | downloader (>= 0.4), GGally, grDevices, graphics, GenomicRanges, XML, Biobase, affy, heatmap.plus, xtable, data.table, EDASeq(>= 2.0.0), RCurl, edgeR(>= 3.0.0), rjson, plyr, CNTools, cghMCR, biomaRt, coin, gplots, ggplot2, survival, stringr (>= 1.0.0), IRanges, scales, rvest, stats, utils, dnet, igraph, supraHex, S4Vectors, SummarizedExperiment, BiocGenerics, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, limma, knitr, devtools, genefilter, ConsensusClusterPlus, RColorBrewer, doParallel, dplyr, parallel, xml2 |
| LinkingTo | |
| Suggests | testthat, png, BiocStyle, rmarkdown |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | TCGAbiolinks_1.0.10.tar.gz |
| Windows Binary | TCGAbiolinks_1.0.10.zip |
| Mac OS X 10.6 (Snow Leopard) | TCGAbiolinks_1.0.1.tgz |
| Mac OS X 10.9 (Mavericks) | TCGAbiolinks_1.0.10.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/TCGAbiolinks/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/TCGAbiolinks/ |
| Package Downloads Report | Download Stats |
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