To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTCGA")

In most cases, you don't need to download the package archive at all.

RTCGA

 

   

The Cancer Genome Atlas Data Integration

Bioconductor version: Release (3.5)

The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.

Author: Marcin Kosinski <m.p.kosinski at gmail.com>, Przemyslaw Biecek <przemyslaw.biecek at gmail.com>

Maintainer: Marcin Kosinski <m.p.kosinski at gmail.com>

Citation (from within R, enter citation("RTCGA")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RTCGA")

Documentation

HTML Integrating TCGA Data - RTCGA Workflow
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DataRepresentation, Preprocessing, RNASeq, Software
Version 1.6.0
In Bioconductor since BioC 3.2 (R-3.2) (1.5 years)
License GPL-2
Depends R (>= 3.3.0)
Imports XML, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales
LinkingTo
Suggests devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr
SystemRequirements
Enhances
URL https://rtcga.github.io/RTCGA
BugReports https://github.com/RTCGA/RTCGA/issues
Depends On Me RTCGA.clinical, RTCGA.CNV, RTCGA.methylation, RTCGA.miRNASeq, RTCGA.mRNA, RTCGA.mutations, RTCGA.PANCAN12, RTCGA.rnaseq, RTCGA.RPPA
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source RTCGA_1.6.0.tar.gz
Windows Binary RTCGA_1.6.0.zip
Mac OS X 10.11 (El Capitan) RTCGA_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/RTCGA/tree/release-3.5
Package Short Url http://bioconductor.org/packages/RTCGA/
Package Downloads Report Download Stats

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