sahilseth/RTCGA.data

Datasets from The Cancer Genome Atlas Project

The family of R packages containing TCGA data

Contribution: Adding a new package to the RTCGA.data family

Data packages submitted to Bioconductor

• RTCGA.mutations
• RTCGA.rnaseq
• RTCGA.clinical

Installation of packages from the RTCGA.data family:

Make sure you have rtools installed on your computer.

# packages that are published to devel version of Bioconductor
BiocInstaller::useDevel() # swiches to devel branchof Bioconductor
source("https://bioconductor.org/biocLite.R") # downloads bioClite function
biocLite("RTCGA.clinical") # installs a package
biocLite("RTCGA.rnaseq")
biocLite("RTCGA.mutations")


# packages not yet published to Bioconductor
if (!require(devtools)) {
   install.packages("devtools")
   require(devtools)
}
install_github("mi2-warsaw/RTCGA.data/PANCAN12")
install_github("mi2-warsaw/RTCGA.data/cnv")

The list of available datasets:

```{Ruby} library(RTCGA.clinical) library(RTCGA.rnaseq) library(RTCGA.mutations) library(RTCGA.PANCAN12) library(RTCGA.cnv) ?clinical ?rnaseq ?mutations ?pancan12 ?cnv ```

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

Installation of the RTCGA package:

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

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

Authors:

Marcin Kosiński, m.p.kosinski@gmail.com

Przemysław Biecek, przemyslaw.biecek@gmail.com