Welcome to RTCGAToolbox.
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 further data analysis.
New version (1.9.4) has been released. See "Update and release notes" below.
New version (1.9.2) has been released. RTCGAToolbox has been accepted by Bioconductor. You may now also access it from: http://www.bioconductor.org/packages/devel/bioc/html/RTCGAToolbox.html
IMPORTANT: Old versions may not be able to get data anymore due to data portal updates! Please update your package to the latest version as soon as possible! (Apr 10, 2015)
Update and release notes
How to install
To install RTCGAToolbox, you may use either "install_github" function from "devtools" (http://cran.r-project.org/web/packages/devtools/index.html) package or you may download, build and install by yourself.
> library("devtools") # You should install devtools package before loading it. > install_github("mksamur/RTCGAToolbox") # This function will download, build and install RTCGAToolbox.
First you need to download archive (zip or tar.gz) by using the links above. After downloading, extract archive file into a folder. Please note that you should have all dependent packages. If you have missing dependent package, you will get an error that tells you which packages you should install. X.Y.Z is the current version of RTCGAToolbox.
$ cd /path/to/folder/ $ R CMD build RTCGAToolbox/ $ R CMD install RTCGAToolbox_X.Y.Z.tar.gz
How to use
User guide can be accessible via the link.
Or you may use following call in R:
vignette(package = "RTCGAToolbox",topic = "RTCGAToolbox-vignette") browseVignettes("RTCGAToolbox")
1.Due to long path names currently Windows OS can not extract data from archives. You may still build and install packages but you can not use getFirehoseData function.
2.In some cases, Mac OS Mavericks may change your tar path.
$ which tar /usr/bin/tar
If you get an error when you call the getFirehoseData function
sh: /usr/bin/gnutar: No such file or directory Error in system(cmd, intern = TRUE) : error in running command
you may change your R configuration and update your tar path for R by using "Sys.setenv (TAR='/usr/bin/tar')"
3.Current version of RTCGAToolbox does not support exon and isoform level data due to high data volume. We are planning to add support for these data types in future updates.
Support or Contact
Having trouble with RTCGAToolbox? Check out the vignette or contact firstname.lastname@example.org and we’ll help you sort it out.
If you have questions or problems about RTCGAToolbox you may visit our FAQ page or you may raise your question to RTCGAToolbox community by using our Q&A Forum.