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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("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: 3.2
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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RTCGAToolbox")
| HTML | RTCGAToolbox | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DifferentialExpression, GeneExpression, Sequencing, Software |
| Version | 2.0.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (0.5 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 | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RTCGAToolbox_2.0.0.tar.gz |
| Windows Binary | RTCGAToolbox_2.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | RTCGAToolbox_2.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | RTCGAToolbox_2.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/RTCGAToolbox/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/RTCGAToolbox/ |
| Package Downloads Report | Download Stats |
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