Data packages not yet submitted to Bioconductor from 2016-01-28 release date of TCGA data.

• RTCGA.mutations.20160128
• RTCGA.rnaseq.20160128
• RTCGA.clinical.20160128
• RTCGA.mRNA.20160128
• RTCGA.miRNASeq.20160128
• RTCGA.RPPA.20160128
• RTCGA.CNV.20160128
• RTCGA.methylation.20160128

Data packages submitted to Bioconductor from 2015-11-01 release date of TCGA data.

• RTCGA.mutations
• RTCGA.rnaseq
• RTCGA.clinical
• RTCGA.PANCAN12
• RTCGA.mRNA
• RTCGA.miRNASeq
• RTCGA.RPPA
• RTCGA.CNV
• RTCGA.methylation

Windows users:

Make sure you have rtools installed on your computer.

# some packages might be still only available on the devel version of Bioconductor
BiocInstaller::useDevel() # swiches to devel branchof Bioconductor - don't use this line if you are interested in release versions
source("https://bioconductor.org/biocLite.R") # downloads bioClite function

Packages from the RTCGA.data - family/factory are based on the RTCGA package

To get started, install the latest version of RTCGA from Bioconductor:

BiocInstaller::useDevel() # swiches to devel branch of Bioconductor
source("https://bioconductor.org/biocLite.R") # downloads bioClite function
biocLite("RTCGA") # installs a package

or use below code to download the development version which is like to be less bugged than the release version on Bioconductor:

if (!require(devtools)) {
    install.packages("devtools")
    require(devtools)
}
install_github("RTCGA/RTCGA", build_vignettes = TRUE)

To check Use Cases run

browseVignettes("RTCGA")

Marcin Kosiński, [email protected]

Przemysław Biecek, [email protected]

Witold Chodor, [email protected]

This repository is synchronized with it's Bioconductor's SVN devel mirror.