To install this package, start R and enter:

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

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

RTCGAToolbox

 

A new tool for exporting TCGA Firehose data

Bioconductor version: Release (3.5)

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Author: Mehmet Kemal Samur

Maintainer: Mehmet Kemal Samur <samur at jimmy.harvard.edu>

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

Installation

To install this package, start R and enter:

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

Documentation

HTML R Script Vignette Title
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DifferentialExpression, GeneExpression, Sequencing, Software
Version 2.6.0
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License GPL (>= 2)
Depends R (>= 3.2.0)
Imports methods, XML, limma(>= 3.18), survival, RCircos, data.table (>= 1.9.4), RCurl, RJSONIO
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, Homo.sapiens
SystemRequirements
Enhances
URL
Depends On Me CVE
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source RTCGAToolbox_2.6.0.tar.gz
Windows Binary RTCGAToolbox_2.6.0.zip
Mac OS X 10.11 (El Capitan) RTCGAToolbox_2.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/RTCGAToolbox/tree/release-3.5
Package Short Url http://bioconductor.org/packages/RTCGAToolbox/
Package Downloads Report Download Stats

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