DOI: 10.18129/B9.bioc.RTCGA    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see RTCGA.

The Cancer Genome Atlas Data Integration

Bioconductor version: 3.7

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")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


To view documentation for the version of this package installed in your system, start R and enter:



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


biocViews DataImport, DataRepresentation, Preprocessing, RNASeq, Software
Version 1.10.0
In Bioconductor since BioC 3.2 (R-3.2) (3 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
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
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
Links To Me
Build Report  

Package Archives

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

Source Package RTCGA_1.10.0.tar.gz
Windows Binary RTCGA_1.10.0.zip
Mac OS X 10.11 (El Capitan) RTCGA_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RTCGA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RTCGA
Package Short Url http://bioconductor.org/packages/RTCGA/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: