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

DOI: 10.18129/B9.bioc.RTCGAToolbox    

This is the development version of RTCGAToolbox; for the stable release version, see RTCGAToolbox.

A new tool for exporting TCGA Firehose data

Bioconductor version: Development (3.6)

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: Marcel Ramos <marcel.ramos at roswellpark.org>

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

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PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DifferentialExpression, GeneExpression, Sequencing, Software
Version 2.7.31
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License file LICENSE
Depends R (>= 3.4.0)
Imports Biobase, BiocGenerics, data.table (>= 1.9.4), GenomicRanges, httr, IRanges, limma(>= 3.18), methods, plyr, RCircos, RCurl, RJSONIO, S4Vectors, survival, XML
LinkingTo
Suggests BiocStyle, Homo.sapiens, knitr, MultiAssayExperiment, readr, rmarkdown
SystemRequirements
Enhances
URL http://mksamur.github.io/RTCGAToolbox/
BugReports https://github.com/mksamur/RTCGAToolbox/issues
Depends On Me
Imports Me
Suggests Me CVE
Build Report  

Package Archives

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

Source Package RTCGAToolbox_2.7.31.tar.gz
Windows Binary RTCGAToolbox_2.7.31.zip
Mac OS X 10.11 (El Capitan) RTCGAToolbox_2.7.31.tgz
Source Repository git clone https://git.bioconductor.org/packages/RTCGAToolbox
Package Short Url http://bioconductor.org/packages/RTCGAToolbox/
Package Downloads Report Download Stats

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